Two Biosensors for the Determination of VEGF-R2 in Plasma by Array SPRi

Vascular endothelial growth factor receptor 2 (VEGF-R2) is a marker of angiogenesis and metastasis of cancer. Two biosensors for the determination of VEGF-R2 in plasma have been developed. One of them is based on a pure gold chip, and the other on a silver/gold bimetallic chip; both have the receptor, monoclonal rabbit antibody specific for human VEGF-R2, attached to the chip via a cysteamine linker. The biosensor with the gold chip exhibits linearity of the analytical signal between 0.03 and 2 ng/mL, a precision of 1.4% and recovery between 99% and 102%. The biosensor with the bimetallic chip exhibits linearity between 0.03 and 1 ng/mL, a precision of 2.2% and recovery between 99% and 103%. Both biosensors tolerate a 1:100 excess of VEGF, VEGF-R1 and VEGF-R3. Both biosensors were validated by parallel determination of VEGF-R2 in 27 different plasma samples using the ELISA immunosensor assay, with very good agreement of the results. Thermodynamic parameters of the interaction of VEGF-R2 with the antibody were determined by QCM (Quartz Crystal Microbalance) and SPRi (Surface Plasmon Resonance imaging) measurements.     

Synthesis of Functionalized Materials Using Aryloxo-Organometallic Compounds toward Spinel-like MM'(2)O(4) (M = Ba(2+), Sr(2+); M' = In(3+), Al(3+)) Double Oxides

The predesigned single-source precursors [Ba{(μ-ddbfo)(2)InMe(2)}(2)] (1), [Me(2)In(μ-ddbfo)](2) (2), [Sr{(μ-ddbfo)(2)AlMe(2)}(2)] (4), and [Me(2)Al(μ-ddbfo)](2) (5) (ddbfoH = 2,3-dihydro-2,2-dimethylbenzofuran-7-ol) for spinel-like double oxides and group 13 oxide materials were prepared via the direct reaction of the homoleptic aryloxide [M(ddbfoH)(4)](ddbfo)(2)·ddbfoH (M = Ba(2+), Sr(2+) (3)) and InMe(3) or AlMe(3) in toluene. In all of the reactions, there was an organometallic-driven abstraction of the OH protons from the 7-benzofuranols in the Ba(2+) and Sr(2+) cation sphere. All compounds were characterized by elemental analysis, (1)H NMR, and FT-IR spectroscopy. In addition, the molecular structures of 1, 2, and 3 were determined by single-crystal X-ray diffraction. The oxide products derived from the compounds mentioned above were studied using elemental analysis, Raman spectroscopy, X-ray powder diffraction, and scanning and transmission electron microscopy equipped with an energy-dispersive spectrometer. Moreover, their specific surface area and mesopore size distribution were evaluated using nitrogen porosimetry. Preliminary investigations of the Eu-doped SrAl(2)O(4) and In(2)O(3) phosphors revealed that the oxides obtained could be considered as matrices for lanthanide ions.     

Quest for zeolite-like metal-organic frameworks: on pyrimidinecarboxylate bis-chelating bridging ligands

Two novel porous zeolitelike metal-organic frameworks (ZMOFs) were constructed via the single metal ion-based molecular building block approach from rigid and directional tetrahedral building units and pyrimidinecarboxylate bridging ligands; their ion exchange and hydrogen sorption properties were evaluated.     

Cobalt-catalyzed asymmetric cyclopropanation with diazosulfones: rigidification and polarization of ligand chiral environment via hydrogen bonding and cyclization

A new D2-symmetric chiral porphyrin P6 (2,6-DiMeO-ZhuPhyrin) with enhanced chiral rigidity and polarity was designed and synthesized through incorporation of hydrogen bonding and cyclic structure. Its cobalt(II) complex [Co(P6)] is a highly active and selective catalyst for asymmetric cyclopropanation of alkenes with diazosulfones. The [Co(P6)]-based catalytic system is suitable for various aromatic olefins as well as electron-deficient olefins, including alpha,beta-unsaturated esters, ketones, and nitriles, forming the corresponding cyclopropyl sulfones under mild conditions in high yields and high selectivities. In most cases, both excellent diastereo- and enantioselectivities were achieved.     

Interplay between acetate ions, peripheral groups, and reactivity of the core nitrogens in transmetalation of tetrapyrroles

The mechanism of acetate-assisted transmetalation of tetrapyrroles was investigated in a model system consisting of chlorophyll a and copper(II) acetate in organic solvents by using a spectroscopic and kinetic approach. Surprisingly, acetate ions bind to the central Mg in chlorophyll much more strongly than do acetonitrile, methanol and even pyridine, one of the best ligands in chlorophyllic systems. This exceptionally strong non-symmetrical axial ligation of the central Mg by acetate causes its out-of-plane displacement and deformation of the tetrapyrrole ring, thus facilitating the interaction with an incoming CuII complex. This mechanism is controlled by a keto-enol tautomerism of the chlorophyll isocyclic ring. Additionally, depending on solvent, acetate activates the incoming metal ions. These new insights allow to suggest a mechanism for the acetate method of metal exchange in tetrapyrrolic macrocycles, which resembles biological insertion of metal ions into porphyrins. It also provides a guideline for the design of more efficient methods for the metalation of porphyrins and related macrocycles.     

Highly recoverable pyridinium-tagged Hoveyda-Grubbs pre-catalyst for olefin metathesis. Design of the boomerang ligand toward the optimal compromise between activity and reusability

Whereas the boomerang ligand of Hoveyda-Grubbs pre-catalysts can be modified by attachment of a pyridinium tag to its benzylidene moiety, a precise adjustment of the length of the spacer allows the optimum balance to be reached between the activity of the catalyst and its recoverability, exceeding 98% after 6 catalytic runs in the best case.     

SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

Accurate prediction of protein secondary structure is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. The accuracy of ab initio secondary structure prediction from sequence, however, has only increased from around 77 to 80% over the past decade. Here, we developed a multistep neural-network algorithm by coupling secondary structure prediction with prediction of solvent accessibility and backbone torsion angles in an iterative manner. Our method called SPINE X was applied to a dataset of 2640 proteins (25% sequence identity cutoff) previously built for the first version of SPINE and achieved a 82.0% accuracy based on 10-fold cross validation (Q(3)). Surpassing 81% accuracy by SPINE X is further confirmed by employing an independently built test dataset of 1833 protein chains, a recently built dataset of 1975 proteins and 117 CASP 9 targets (critical assessment of structure prediction techniques) with an accuracy of 81.3%, 82.3% and 81.8%, respectively. The prediction accuracy is further improved to 83.8% for the dataset of 2640 proteins if the DSSP assignment used above is replaced by a more consistent consensus secondary structure assignment method. Comparison to the popular PSIPRED and CASP-winning structure-prediction techniques is made. SPINE X predicts number of helices and sheets correctly for 21.0% of 1833 proteins, compared to 17.6% by PSIPRED. It further shows that SPINE X consistently makes more accurate prediction in helical residues (6%) without over prediction while PSIPRED makes more accurate prediction in coil residues (3-5%) and over predicts them by 7%. SPINE X Server and its training/test datasets are available at http://sparks.informatics.iupui.edu/