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.     

An improvement in the bending ability of a hinged trisaccharide with the assistance of a sugar-sugar interaction

Hinged di- and trisaccharides incorporating 2,4-diamino-beta-D-xylopyranoside as a hinge unit (Hin) were synthesized. Bridging of the diamino group of Hin by carbonylation or chelation to a metal ion results in a conformational change from (4)C1 to (1)C4, which in turn causes a bending of the oligosaccharides. In this study, the bending abilities of the hinged oligosaccharides were compared, in terms of the reactivities toward carbonylation and chelation. Di- or trisaccharides containing a 6-O-glycosylated mannopyranoside or galactopyranoside at their reducing ends had bending abilities similar to that of the Hin monosaccharide, probably because there were neither attractive nor repulsive interactions between the reducing and nonreducing ends. However, when Hin was attached at O2 of methyl mannopyranoside (Man alphaMe), the bending ability was dependent on the nonreducing sugar and the reaction conditions. Typically, a disaccharide--Hin beta(1,2)Man alphaMe--was difficult to bend under all the tested reaction conditions, and the bent population in the presence of Zn(II) was only 4%. On the other hand, a trisaccharide--Man alpha(1,3)Hin beta(1,2)Man alphaMe--was bent immediately after the addition of Zn(II) or Hg(II), and the bent population reached 75%, much larger than those of all the other hinged trisaccharides ever tested (<40%). This excellent bending ability suggests an attractive interaction between the reducing and nonreducing ends. The extended conformation was recovered by the addition of triethylenetetramine, a metal ion chelator. Reversible, quick, and efficient bending of the hinged trisaccharide was thus achieved.     

An improved procedure for the conversion of indolines into indoles

The addition of a sacrificial enamine (such as indole), or of a vinyl ether (like dihydropyran) to an indoline during dehydrogenation by phenylseleninic anhydride dramatically improves the yield of the corresponding indole. This is due to scavenging of Se¹¹ phenylselenenating species.     

Synthetic studies on carbapenem antibiotics from penicillins. IV. Stereoselective kinetic protonation of a chiral azetidinone enolate

A stereoselective kinetic protonation of the azetidinone enolate $\text{B}$ was studied and an efficient synthesis of$\text{2}$(cis) was achieved via aldol reaction of $\text{5}$ with acetone followed by the kinetic protonation with Ph₃SnH as proton source.     

Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen

The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.     

Ferrocene-containing polymers. I. Radiation-induced polymerization of ferrocenylmethyl methacrylate

γ-Ray-induced polymerizations of ferrocenylmethyl methacrylate (FMMA) in crystalline and amorphous states were investigated with kinetical and ESR methods. In the crystalline state the polymerization of FMMA proceeded slowly and gave low-molecular-weight polymers, whereas in the amorphous state it proceeded rapidly and gave polymers of much higher molecular weight. Molecular weight distributions of these polymers were binodal. The temperature dependence and the dose-rate dependence of the polymerization rates were different between the two states. Wide-line nuclear magnetic resonance (NMR) spectra of the amorphous monomer suggested that the polymerization proceeded in a supercooled state. Electron spin resonance (ESR) spectra of γ-irradiated FMMA and 1,1′-ferrocenyl-di(methyl methacrylate) showed that ferrocene radicals and methacrylic radicals were formed simultaneously at low temperature; with increasing temperature the former radicals disappeared, whereas the latter changed into growing chain radicals. The yields of radicals were relatively low; this means that ferrocene groups in the monomers behave as a radiation energy absorber.     

On-line column preconcentration for the determination of cobalt in sea water by flow-injection chemiluminescence detection

A flow-injection method for the determination of dissolved cobalt(II) in sea water has been studied based on a combination of column preconcentration using 8-quinolinol immobilized on silica gel, fluoride containing metal alkoxide glass (8HQ-MAF) and chemiluminescence detection with a gallic acid-hydrogen peroxide system. Co(II) is selectively recovered from an acidified sample with 8-quinolinol immobilized on silica gel. After elution with dilute hydrochloric acid the resultant eluent is mixed with the reagent solutions, heated to 60^°C and then introduced into the CL cell. The analysis time including the 2-min sample load was 8 min per sea water sample with a corresponding detection limit of 0.62 ngl^-1 (3). The average standard deviation calculated for 10 replicate measurements of artificial sea water samples with a concentration of 10 ngl^-1 cobalt was ±2.1%. The method has been tested with the standard reference sea waters NASS and CASS.