Construction of Human Nonimmune Library and Selection of scFvs Against IL-33

Interleukin (IL) 33 plays very important roles in inflammatory and allergic diseases. To select human single-chain Fv fragments (scFvs) against IL-33, a nonimmune phage library system was constructed. The full-length cDNA library was synthesized for amplification of the variable heavy chain (V_H) and variable light chain (V_L). By overlapping extension PCR for splicing V_H and V_L, the full-length scFv library DNA were amplified and then transformed into Escherichia coli TG1. The scFv library was constructed successfully which contained 2.5?×?10⁸ independent clones with full-length scFv inserts. The results of fingerprint maps of the scFvs by BstN I and DNA sequencing from the library at random proved that the library was diverse. The human IL-33 was amplified, expressed, and purified. The purified IL-33 with bioactivity was biotinylated and used as antigen for selection of scFv library by phage display. After three rounds of affinity selection, about 30?% of clones have specific binding activity with IL-33. Five of those with good binding activity were transformed into E. coli strain HB2151 for soluble expression. The selected scFvs were further identified by western blot and sequencing. Those selected scFvs could be used for further research of their effect on inflammatory and allergic diseases such as asthma by blockade of IL-33.     

Construction of Hierarchical Nanotubes Assembled from Ultrathin V3S4@C Nanosheets towards Alkali‐Ion Batteries with Ion‐Dependent Electrochemical Mechanisms

Ultrathin core–shell V₃S₄@C nanosheets assembled into hierarchical nanotubes (V₃S₄@C NS‐HNTs) are synthesized by a self‐template strategy and evaluated as general anodes for alkali‐ion batteries. Structural/physicochemical characterizations and DFT calculations bring insights into the intrinsic relationship between crystal structures and electrochemical mechanisms of the V₃S₄@C NS‐HNTs electrode. The V₃S₄@C NS‐HNTs are endowed with strong structural rigidness owing to the layered VS₂ subunits and interlayer occupied V atoms, and efficient alkali‐ion adsorption/diffusion thanks to the electroactive V₃S₄‐C interfaces. The resulting V₃S₄@C NS‐HNTs anode exhibit distinct alkali‐ion‐dependent charge storage mechanisms and exceptional long‐durability cyclic performance in storage of K⁺, benefiting from synergistic contributions of pseudocapacitive and reversible intercalation/de‐intercalation behaviors superior to those of the conversion‐reaction‐based Li⁺‐/Na⁺‐storage counterparts.     

A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations

We describe a simple and rapid algorithm for generating data structures and starting coordinates of polynucleotides for potential energy calculations. The algorithm is tailored to investigations in cartesian coordinate, rather than dihedral angle, space. First, instead of a tree structure for molecular design, we set up a helix from a simple list of bonds for the basic DNA subunits (sugar, phosphate, and bases). Second, instead of using successive transformations to obtain a set of coordinates in one reference frame, we apply a simple “matching” routine to patch DNA subunits. Third, we avoid ring closure and geometry optimization by allowing deviations from equilibrium values only for P? O3′ bond lengths and O5′? P? O3′ bond angles at the residue connection sites. A double-stranded helix is constructed from duplex building blocks (2 hydrogen-bonded nucleotides) which are in turn built from the basic structural units. Every building block is constructed from two sets of geometric variables: {α, β, γ, χ, P, τ_max}, one for each strand. The building blocks are then assembled into a helix by using the 6 rigid body transformations {Δx, Δy, Δz, Θ_ROLL , Θ_TILT , Θ_TWIST }. For cartesian space programs, generating starting coordinates by this procedure is particularly useful as an alternative to using actual crystal structure coordinates. After describing the algorithm in detail, we illustrate how it was used to generate model A, B, and Z DNA helices. We conclude by suggesting how the algorithm can be used to pursue a build-up technique and to set up a wide range of starting conformations in the goal of locating novel helical structures.     

The vanadate garnet Ca2NaCd2V3O12: a single‐crystal X‐ray diffraction study

Single crystals of the vanadate garnet Ca₂NaCd₂V₃O₁₂ (dicalcium sodium dicadmium trivanadate) were synthesized using the floating‐zone method and the crystal structure was investigated using single‐crystal X‐ray diffraction. We considered the effectiveness of substitution of the Y‐site cation with reference to previous structural studies of vanadate garnets. The structures of vanadate garnets are subject to geometric constraints similar to those of silicate garnets. These constraints force the tetrahedral–dodecahedral shared edge length in vanadate garnets to become shorter than the unshared dodecahedral edge length, as in ugrandite (uvarovite, grossular and andradite) garnets. However, the vanadate garnet Ca₂NaCd₂V₃O₁₂ exhibits the normal structural feature, similar to pyralspite (pyrope, almandine and spessartine) garnets, namely that the dodecahedral–dodecahedral shared edge length is shorter than the unshared dodecahedral edge length. With increasing ionic radius of the Y‐site cation, the atomic coordinates x, y and z of oxygen adopt values which satisfy Pauling's third rule.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.     

胶体模板法制备有序大孔TiO2材料

以单分散的聚甲基丙烯酸甲酯(PMMA)微球为胶体模板, 采用钛酸丁酯、水、乙醇、盐酸等配成的混合溶胶填充在微球间间隙, 经水解形成凝胶, 然后通过程序升温焙烧去掉单分散的PMMA微球, 可得有序TiO₂大孔材料. 实验结果表明, 溶胶的配比为V(钛酸丁酯)∶V(水)∶V(乙醇)∶V(盐酸)＝5∶2∶3∶1, 在空气中凝胶20 h. 去掉单分散的PMMA微球的程序升温控制的条件为1 ℃/min的升温速率升到250 ℃恒定3 h, 再以2 ℃/min的升温速率升到450 ℃恒定8 h, 最后以10 ℃/min的降温速率降到室温.     

Crystal structure and the role of cation group factor in the third‐order nonlinear optical properties of cadmium complexes constructed by 1,3‐dithiole‐2‐thione‐4,5‐dithiolato ligand

A cadmium complex bis(benzyltriethylammonium) bis(1,3‐dithiole‐2‐thione‐4,5‐dithiolato)‐cadmium(II) ((TEBA)₂[Cd(DMIT)₂]) has been synthesized and its crystal structure has been determined by means of X‐ray single‐crystal diffraction. The central cadmium(II) ion coordinates with two DMIT, which constructed a distorted tetrahedron environment. Its third‐order nonlinear optical properties have been studied using Z‐scan technique with 20 ps pulses at wavelength 1064 nm. Its third‐order nonlinear susceptibility χ⁽³⁾ value was determined to be 1.24 × 10⁻¹⁹ m² V⁻², the figure of merit, χ⁽³⁾/α₀, was estimated to be 2.64 × 10⁻²⁰ m³ V⁻². Copyright © 2011 John Wiley & Sons, Ltd.     

Structures with vacancy sublattices based on fcc and bcc packings of spheres and their stability at negative pressures

Structures with regular sublattices of vacancies, vacancy clusters, and channels constructed from the fcc and bcc packings of spheres were analyzed. Homologous series of structures were constructed, and formulas were derived to correlate the basic structural characteristics with the composition of the “vacancy compounds” A _m V _n . The thermodynamic stabilities of structures with vacancies were compared with the stability of a flaw-free structure in the range of negative pressures using the simple interatomic interaction potential. Structures with vacancy clusters and channels may be more stable than the ideal structure in a certain range of pressures. This paper summarizes the results of simulations of structures with vacancy sublattices based on close packings of spheres described in this work and previous publications and their thermodynamic stability at negative pressures.     

Molecular dynamics simulation of the structure and thermodynamic properties of liquid rubidium at pressures of up to 10 GPa and temperatures of up to 3500 K

The models of rubidium at temperatures of up to 3500 K, degrees of compression of up to Y = V/V₀ = 0.3, and pressures of up to 32 GPa were constructed by molecular dynamics (MD) using the interparticle potential ЕАМ. The thermodynamic properties of the MD models agree satisfactorily with experiment in the range of parameters under study at rubidium densities higher than 0.86 g/cm³. The behavior of the models in the range of the van der Waals loop was analyzed; the calculated critical temperature of rubidium T_c is ～2250 ± 25 K, density ～0.41 g/cm³, pressure ～0.019 GPa, and compressibility factor Z = pV/RT ≈ 0.137. The states with the unity factor Z = 1 were observed at pressures of up to 0.30 GPa (at ～3000 K); the temperature dependence of the density of the models with Z = 1 is nearly linear, and the Boyle temperature is T_B ≈ 10160 K. The ratio T_c/T_B = 0.221 is close to this value for cesium (0.23) and mercury (0.276). In the temperature and pressure ranges under study, the inversion of the Joule–Thomson coefficient did not take place, but should be observed at pressures of ?0.3 GPa and elevated temperatures. It was found that the diffusion coefficient D(T) dependences do not straighten in the usually used coordinates within wide temperature ranges. It was concluded that the structure of the liquid smoothly changes when the rubidium models are compressed and this reveals in the change of the degree of asymmetry of the first peak of the radial distribution function.     

Facile synthesis of Li3V2(Po4)3/C nano-flakes with high-rate performance as cathode material for Li-ion battery

The flake-like Li₃V₂(PO₄)₃/C has been successfully synthesized by rheological phase method using polyvinyl alcohol (PVA) as template; the Li₃V₂(PO₄)₃/C without PVA assistance has been prepared for comparison. X-ray diffraction analysis shows that the two samples are well crystallized, and no impurity phases are detected. The scanning electron microscopy results reveal that there is a significant difference in morphologies between PVA-assisted sample and sample without PVA; the former shows a flake-like morphology, while the latter presents regular granular shape with some agglomeration. Transmission electron microscopy images reveal that Li₃V₂(PO₄)₃ particles are coated with a uniform surface carbon layer. The lattice fringes with a spacing of 0.428 nm can be clearly seen from the high-resolution transmission electron microscopy image. The PVA-assisted sample shows a discharge capacity of 120, 110, and 96 mAh g^?1 at 1 C, 20 C, and 50 C, respectively; however, the sample without PVA exhibits a lower discharge capacity. Based on the analysis of electrochemical impedance spectroscopy, the lithium ion diffusion coefficients of Li₃V₂(PO₄)₃/C and PVA-assisted Li₃V₂(PO₄)₃/C are 4.19?×?10^?9 and 4.99?×?10^?8 cm² s^?1, respectively. In summary, it is demonstrated that using PVA as a template can obtain flake-like morphology and significantly improve the comprehensive electrochemical performances of Li₃V₂(PO₄)₃/C cathode material.     

Hydrothermal Synthesis of Unique Hollow Hexagonal Prismatic Pencils of Co3V2O8⋅n H2O: A New Anode Material for Lithium‐Ion Batteries

Hollow structures of transition‐metal oxides, particularly mixed‐metal oxides, could be promising for various applications such as lithium‐ion batteries (LIBs). Compared to the synthesis of metal oxide hollow spheres by the template method, non‐spherical metal oxide hollow hexagonal polyhedra have not been developed to date. Herein, we report the controlled hydrothermal synthesis of a new phase of Co₃V₂O₈?n H₂O hollow hexagonal prismatic pencils (HHPPs), which is composed of uniform structural units. By varying the amount of NaOH in the presence of NH₄⁺ and without any template or organic surfactant, the hexagonal prismatic pencils gradually transform from solid into hollow structures, with sizes varying from 5 to 20 μm. The structure of pencils can be preserved only in a limited range of the molar ratio of OH^?/NH₄⁺. As a new anode material for LIBs, such hollow pencils exhibit impressive lithium storage properties with high capacity, good cycling stability, and superior rate capability.     

Phase diagram and IR spectral investigations of the 2TeO2 · V2O5Li2O · V2O5 · 2TeO2 system

By means of X-ray phase analysis, IR spectroscopy, and DTA, the system 2TeO₂ · V₂O₅Li₂O · V₂O₅ · 2TeO₂ was investigated and its phase diagram was constructed. The formation of a new compound with composition Li₂O · 3V₂O₅ · 6TeO₂, melting incongruently was documented. A comparison of the bands in the IR spectrum was made. Stable glasses in the whole range of concentrations were prepared. From the IR spectra of the glasses, the corresponding crystallization products, and the data of known crystal structures, a model of the short-range order in the glasses was proposed.     

Two new transition-metal complexes (TMCs)-templated three-dimensional supramolecular networks based on tungstovanadophosphates

Two new polyoxometalates [Ni(phen)₃][Ni(en)₃][Ni(en)₂(H₂O)₂][Ni(en)₂]_0.5[PW^VI₇W^V₂V^IV₃O₄₀(V^IVO)₂]·6H₂O (1) and [Ni(phen)₃]₂[Ni(en)₂]Na[PW^VI₇W^V₂V^IV₃O₄₀(V^IVO)₂]·8H₂O (2) (en=ethylenediamine, phen=1,10-phenanthroline) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction, IR, EPR, XPS, elemental analysis and thermogravimetry. Their structures exhibit interesting 3D supramolecular networks, and contain new bicapped (pseudo-) Keggin-type tungsten-vanadium cluster and the template transition-metal complexes (TMCs) being generated in situ under mild hydrothermal conditions. Interestingly, compound 1 contains four different kinds of nickel complex countercations.     

Protein-Loop Mimetics: A Diketopiperazine-Based Template to Stabilize Loop Conformations in Cyclic Peptides Containing the NPNA and RGD Motifs

We explore here an approach to mimic the structures and biological functions of protein loops in small synthetic molecules, by grafting the loop of interest onto an organic template comprising a bicyclic diketopiperazine, prepared by the formal coupling of (2S,4S)-4-aminoproline (Pro(NH₂)) and aspartic acid (Asp). The Fmoc-protected template 4 is used to prepare cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵- Ala⁶-Temp-) ( 5 ) and cyclo(-Ala¹-Arg²-Gly³-Asp⁴-Temp-) ( 6 ) (where Temp = template derived from 4 ), containing the Asn-Pro-Asn-Ala (NPNA) and Arg-Gly-Asp (RGD) motifs. The conformational properties of these molecules are studied in aqueous solution by NMR and simulated-annealing methods. The NPNA motif, an immunodominant epitope on the circumsporozoite surface protein of the malaria parasite Plasmodium falciparum, is shown to adopt a stable type-I β-turn in 5 . The template in 5 adopts a preferred conformation with Pro(NH₂)χ₁ ≈? ?35° and the Asp moiety χ₁ ≈? 70°. A different template conformation is inferred for 6 , with Pro(NH₂)χ₁ ≈? 0°, but the ARGD loop appears by NMR to undergo rapid conformational averaging. Solid-phase binding assays reveal that 6 displays modest antagonist activity towards both the integrin α_IIbβ₃ and α_vβ₃ receptors.     

[NH3(CH2)6NH3][P2V5O17]·3.83H2O: A new 3D Organic‐templated Vanadophosphate with Extra‐large 16‐Membered Ring Constructed from Nanosized P–O–V Wheels

A new porous 3D vanadophosphate, [NH₃(CH₂)₆NH₃][P₂V₅O₁₇] · 3.83H₂O ( 1 ) is synthesized by using NH₂(CH₂)₆NH₂ as template, and characterized by single crystal structural analysis, X‐ray diffraction, IR spectroscopy, TG analysis, and powder XRD. Single crystal analysis shows that compound 1 crystallizes in cubic shape, space group Im m with cell dimensions: a = b = c = 26.5068(8) Å, V = 18624.0(10) Å³, Z = 24. Structural refinement indicates that the inorganic framework of 1 is constructed from nanosized P–O–V wheels.     

Modeling the active centers of V<Subscript>2</Subscript>O<Subscript>5</Subscript>/SiO<Subscript>2</Subscript> and V<Subscript>2</Subscript>O<Subscript>5</Subscript>/TiO<Subscript>2</Subscript> supported catalysts. DFT theoretical analysis of optical properties

Within the framework of the density functional theory (DFT), the electronic structure of monooxodioxovanadium functional groups in tetrahedral coordination, which model the active centers (ACs) of fine supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂, has been analyzed. The optimal structures of three ACs as possible models of monomeric and polymeric oxovanadium forms on the carriers with low vanadium content were determined. The modified DFT method involving the time dependence of Kohn-Sham equation (TDDFT) was used for the adopted AC models to calculate the energies of the excited states, and optical spectra of the absorption in 25000–60000 cm^?1 region were reconstructed on their base. The spectrum in this region is due to O → V charge transfer. The features of electronic spectra with the charge transfer for V₂O₅/SiO₂ and V₂O₅/TiO₂ catalysts and the vibrational spectra of three AC models corresponding to the monomeric and dimeric oxovanadium forms of the supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂ were defined. The detailed interpretation of normal vibration frequencies is given. The frequencies typical of the monomeric and dimeric oxovanadium forms on the carrier surface were identified.     

Cerium(IV)‐Driven Water Oxidation Catalyzed by a Manganese(V)–Nitrido Complex

The study of manganese complexes as water‐oxidation catalysts (WOCs) is of great interest because they can serve as models for the oxygen‐evolving complex of photosystem II. In most of the reported Mn‐based WOCs, manganese exists in the oxidation states III or IV, and the catalysts generally give low turnovers, especially with one‐electron oxidants such as Ce^IV. Now, a different class of Mn‐based catalysts, namely manganese(V)–nitrido complexes, were explored. The complex [Mn^V(N)(CN)₄]²⁻ turned out to be an active homogeneous WOC using (NH₄)₂[Ce(NO₃)₆] as the terminal oxidant, with a turnover number of higher than 180 and a maximum turnover frequency of 6 min⁻¹. The study suggests that active WOCs may be constructed based on the Mn^V(N) platform.     

The template synthesis of mesoporous silicas with the thiourea functional group

Mono- and bifunctional mesoporous silicas containing the thiourea group ≡Si(CH₂)₃NHC(S)NHC₂H₅ or thiourea and various nitrogen-containing groups [≡Si(CH₂)₃NH₂, ≡Si(CH₂)₃NH(CH₂)₂NH₂, or {≡Si(CH₂)₃}₂NH], respectively, in the surface layer were prepared by template syntheses with cetylpyridinium chloride as a template. The synthesized samples had well-developed porous structures (S _sp = 750–1150 m²/g, V _c = 0.51–0.72 cm³/g, and d = 2.4–3.5 nm) and high functional group contents (1.0–2.0 mmol/g). Hydrothermal treatment of the mesophases in a mother liquor at 80°C (24 h) improved the structure-adsorption characteristics of the functionalized mesoporous silicas.