Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

Characteristics of organic transformations in a confined dendritic core: studies on the AIBN-initiated reaction of dendrimer cobalt(II) porphyrins with alkynes

Cobalt(II) complexes of poly(aryl ester) dendrimer porphyrins [(m-[Gn]TPP)Co(II)] (generation number n=0-4), in the presence of azobisisobutyronitrile (AIBN) at 60 degrees C, underwent alkenylation with several alkynes at the metal center. A complete inhibition of double-bond migration (secondary transformation) was observed for [(m-[Gn]TPP)Co(II)] (n=3 and 4), which gave [(m-[Gn]TPP)Co(III)-C(=CH(2))R] (n=3 and 4) exclusively. Overall reaction rates for [(m-[Gn]TPP)Co(II)] (n=0-3) were hardly dependent on the size of the dendritic substituents, while a notable retardation was observed for the largest dendrimer, [(m-[G4]TPP)Co(II)]. Mechanistic studies on double-bond migration with pure [(m-[Gn]TPP)Co(III)-C(=CH(2))Bu] (n=0-4) demonstrated that the secondary transformation involves participation of [(m-[Gn]TPP)Co(III)H] (n=0-4), derived from [(m-[Gn]TPP)Co(II)] and AIBN, rather than [(m-[Gn]TPP)Co(II)] alone. Crossover experiments using [(m-[Gn]TPP)Co(III)-C(=CH(2))Bu] (n=2-4), in combination with nondendritic [(m-[G0]TPP)Co(II)] and AIBN, indicated a high level of steric protection of the active center by a robust [G4]-dendritic cage, as suggested by a (1)H NMR pulse relaxation time profile of m-[G4]TPPH(2).     

A Three-Center Orbital Interaction in the Diels-Alder Reactions Catalyzed by Lewis Acids

Ab initio calculations were performed on title reactions between butadiene and acrolein with BCl(3), AlCl(3), GaCl(3), InCl(3), ZnCl(2), SnCl(2), and SnCl(4). A dimethyl ether molecule is explicitly considered in various reaction systems to examine solvent effects. First, the reaction path of an AlCl(3)-promoting reaction was examined thoroughly. This reaction has two channels. The first one involves a weak reactant-like complex (precursor) and a normal [4 + 2] addition. The second does three elementary processes, one-center addition, ring closing, and Claisen shift. The first channel is more favorable by 12.1 kcal/mol (B3LYP/6-311+G(2d,p) SCRF//B3LYP/6-31G SCRF) than the second one. Then the first channels with other Lewis acids were traced with and without an ether molecule. The ether molecule has an appreciable effect not on geometries but on activation energies. BCl(3) is desolvated and has extraordinarily strong catalytic ability. Even with the strongest catalyst, not a [2 + 4] but a normal [4 + 2] cycloaddition takes place. Except for BCl(3), SnCl(4) is the strongest Lewis acid with the ether molecule. The frontier orbital, LUMO, of acrolein is distorted in the course of the reaction so that the formation of two C-C covalent bonds is possible. The precursor formation and the one-center addition were discussed also by the frontier orbital theory.     

Correlation between the structure of water in the vicinity of carboxybetaine polymers and their blood-compatibility

The structure and hydrogen bonding of water in the vicinity of carboxybetaine homopolymer (poly[1-carboxy-N,N-dimethyl-N-(2'-methacryloyloxyethyl)methanaminium inner salt] (PolyCMB), and a random copolymer of CMB and n-butyl methacrylate, Poly(CMB-r-BMA), with various molecular weights were analyzed in their aqueous solutions and thin film with contours of O-H stretching of Raman and attenuated total reflection infrared (ATR-IR) spectra, respectively. The relative intensity of the collective band (C value) corresponding to a long-range coupling of O-H stretchings of the Raman spectra for aqueous solution of Poly(CMB-r-BMA) was very close to that for pure water, which is in contrast with the smaller C value in aqueous solution of ordinary polyelectrolytes. The number of hydrogen bonds collapsed by the presence of one monomer residue (N(corr) value) of PolyCMB and Poly(CMB-r-BMA) (CMB, 45 mol %) (M(w), 1.14 x 10(4) and 1.78 x 10(4), respectively) could be calculated from the C value. The N(corr) values were much smaller than those for ordinary polyelectrolytes and close to those for nonionic water-soluble polymers such as poly(ethylene glycol) and poly(N-vinylpyrrolidone). Furthermore, a water-insoluble Poly(CMB-r-BMA) with a large BMA content (M(w) = 347 kD, CMB 27 mol %) could be cast as a thin film (thickness, ca. 10 microm) on a ZnSe crystal for the ATR-IR analyses. At an early stage of sorption of water into the Poly(CMB-r-BMA) film, the O-H stretching band of IR spectra for the water incorporated in the film was similar to that for free water, which is in contrast with the drastic change in the O-H stretching band of water incorporated in polymer films such as poly(methyl methacrylate) (PMMA) and poly(n-butyl methacrylate) (PBMA). The theoretical vibrational frequency for water molecules hydrating a betaine molecule calculated by using a density functional method supported the experimental results. The adhesion of human platelets to Poly(CMB-r-BMA) films was much less than that to PMMA and PBMA. With an increase in the content of CMB residue, the number of platelets adhered to the Poly(CMB-r-BMA) film drastically decreased and then gradually increased, probably due to the increase in the roughness of the film surface. These results suggest that the carboxybetaine monomer residues with a zwitterionic structure do not significantly disturb the hydrogen bonding between water molecules in both aqueous solution and thin film systems, resulting in the excellent blood-compatibility of the carboxybetaine polymers.     

Molar enthalpies of transfer of divalent transition metal lons and their chloro complexes from N,N-dimethylformamide to N,N-dimethylacetamide

The molar enthalpies of transfer _t H ^° of some divalent metal ions (M-Mn, Co, Ni and Zn) and their chloro complexes from N,N-dimethyl-for-mamide (DMF) to N,N-dimethylacetamide (DMA) have been determined using the tetraphenylarsonium-tetraphenylborate (TATB) assumption at 25°C. Although physicochemical properties of DMF and DMA as solvent are similar, the _t H ^°(M ²⁺) value increased significantly in the order Mnt H ^° values for the mono-and dichloro complexes showed also a strong metal dependence, while those for the triand tetrachloro complexes practically do not. These results can be reasonably explained in terms of steric hindrance upon solvation of the metal ions and complexes in DMA.     

Correction to: Asymptotic Normality for Inference on Multisample,High-Dimensional Mean Vectors Under Mild Conditions

Methodology and Computing in Applied Probability -     

An infeasible interior-point arc-search algorithm for nonlinear constrained optimization

Numerical Algorithms - In this paper, we propose an infeasible arc-search interior-point algorithm for solving nonlinear programming problems. Most algorithms based on interior-point methods are...     

Isolation and Stereostructures of Dolastatin G and Nordolastatin G, Cytotoxic 35-Membered Cyclodepsipeptides from the Japanese Sea Hare Dolabella auricularia

A bioassay-directed fractionation of the cytotoxic constituents of the Japanese sea hare Dolabella auricularia resulted in the isolation of two 35-membered depsipeptides dolastatin G (1) and nordolastatin G (2), which showed cytotoxicity against HeLa S(3) cells with IC(50) values of 1.0 and 5.3 &mgr;g/mL, respectively. The gross structures of these substances were established by spectroscopic analysis including 2D NMR techniques. The absolute stereostructure of 1 was determined by chiral HPLC analysis of amino acid components obtained from acid hydrolysis of 1 and by the enantioselective syntheses of two degradation products arising from polyketide portions. Nordolastatin G (2) is a congener that has the same absolute stereochemistry as that of 1.     

Fluorinated polysilanes. Palladium catalyzed 1,4-addition of fluorodisilanes to conjugated diene and enone systems

In the presence of palladium complexes as catalysts, fluorinated disilanes add to 1,3-dienes, metehyl vinyl ketone and p-benzoquinone to give mainly 1,4-addition products.     

Syntheses of polyurethanes derived from oximes and their photodegradation

Polyoxime-urethanes have been synthesized from dioximes and diisocyanates, and their structures have been ascertained by elemental analysis and infrared spectroscopy. They can be represented by the general formula: These polymer films were photolyzed by using a high-pressure 100-W mercury lamp, and the rate of decomposition of the N? O bond was determined by use of ultraviolet and infrared spectra, or comparing the photochemical behavior with that of corresponding model compounds. Upon irradiating these polymers in the presence or absence of sensitizers or a hydrogen donor, there were obtained photolyzed polymers of low molecular weight, of which the molecular weights were estimated by observing the viscosity changes. To deduce the mechanism of photodegradation of polyoxime-urethane, photolysis of benzophenone oxime-phenyl urethane was investigated as a model compound.