A deterministic algorithm for constrained enumeration of transmembrane protein folds

A deterministic algorithm for enumeration of transmembrane protein folds is presented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations, which can be scored and refined as part of a process designed for computational elucidation of transmembrane protein structures.     

Microchip electrophoretic protein separation using electroosmotic flow induced by dynamic sodium dodecyl sulfate-coating of uncoated plastic chips

Separation of sodium dodecyl sulfate (SDS)-protein complexes is difficult on plastic microchips due to protein adsorption onto the wall. In this paper, we elucidated the reasons for the difficulties in separating SDS-protein complexes on plastic microchips, and we then demonstrated an effective method for separating proteins using polymethyl methacrylate (PMMA) microchips. Separation difficulties were found to be dependent on adsorption of SDS onto the hydrophobic surface of the channel, by which cathodic electroosmotic flow (EOF; reversed flow) was generated. Our developed method effectively utilized the reversed flow from this cathodic EOF as a driving force for sample proteins using permanently uncoated but dynamic SDS-coated PMMA microchips. High-speed (6 s) separation of proteins and peptides up to 116 kDa was successfully achieved using this system.     

Starburst dendrimer-supported pseudostationary phases for electrokinetic chromatography

Pseudo-stationary phases for electrokinetic chromatography were prepared by the alkylation of starburst dendrimers (SBDs). The SBD-supported pseudo-stationary phase with dodecyl groups showed higher efficiency than short-akyl derivatives, and maintained the hydrophobic property inthe presence of methanol. The dodecyl-modified SBD provided wide migration time windows ar high methanol content to effect the separation of sixteen aromatic hydrocarbons, the priority pollutants designated by EPA, in 65% methanol. The selectivity of polymer-supported pseudo-stationary phase can be varied simply by changing the length of the alkyl groups. The dodecyl SBD showed relatively similar selectivity as sodium dodecyl culfate micelle, whereas short alkyl derivatives showed preference towards rigid and planar compounds based on the rigid and planar compounds based on the rigid polymer backbones. The selectivity of SBD-supported pseudo-stationary phases was dominated by the chain length of the alkyl groups, with the minor effect of the structure of the core and the generation of SBD where alkyl groups were attached.     

Preconcentration of palladium(II) from water with thionalide loaded on silica gel

2-Mercapto-N-2-naphthylacetamide (thionalide) on silica gel is used for rapid preconcentration of μg l^?1 levels of palladium(II) from aqueous solution, followed by atomic absorption spectrometric measurement. In batch experiments, palladium was quantitatively retained on the gel from solutions 5 M in acid to pH 8; equilibrium was achieved within 10 s. The chelating capacity of the gel was 7.5 μmol Pd g^?1 at pH < 4. The effect of flow rate on retention was studied. Palladium retained on the column was completely eluted with 20 ml of 0.2 M thiourea in 0.1 M hydrochloric acid. The palladium concentration in sea water is shown to be < 0.3 μg l^?1.     

Dehydrogenation of ethylbenzene with CO2 over Cr-MCM-41 catalyst

M-MCM-41 catalysts (M: V, Cr, Fe, and Ga) prepared by direct hydrothermal synthesis (DHT) have been tested for dehydrogenation of ethylbenzene with CO₂. The synthesized materials were characterized by X-ray diffraction (XRD), N₂ adsorption (77 K), and diffuse reflectance UV–vis spectroscopic measurements. Cr-MCM-41 showed the highest activity among M-MCM-41 catalysts tested, resulting in the production of styrene with the conversion of 65% and the selectivity above 90%. The rate of styrene formation increased with increasing Cr loading up to 1.7 wt.%. It is suggested that Cr(VI)O₄ in tetrahedral coordination is formed as an active monochromate species and reduced to Cr(III)O₆ in octahedral coordination as a less active polychromate species during the reaction. Deactivated catalyst was regenerated by a treatment with gaseous oxygen or CO₂, during which redistribution as well as reoxidation of polymeric Cr(III)O₆ octahedra to monomeric Cr(VI)O₄ tetrahedra was observed. The rate of CO formation increased together with that of styrene formation, while the rate of H₂ formation decreased, with increasing partial pressure of CO₂. It was confirmed that reverse water-gas shift reaction took place over Cr-MCM-41 by a separate experiment. The rate of CO formation during the dehydrogenation of ethylbenzene with CO₂ over Cr-MCM-41 was well accounted for by assuming parallel occurrence of two reactions, i.e., direct oxidative dehydrogenation of ethylbenzene with CO₂ and simple dehydrogenation of ethylbenzene thermodynamically assisted by reverse water-gas shift reaction.     

Electronic structures of exohedral lanthanide-C60 clusters

We have studied the electronic structures of several gas phase exohedral lanthanide (Ln)-C(60) clusters, Ln(n)C(60) (Ln=Pr, Ho, Tb, Tm, Eu, and Yb) with n=1-4, by photoionization spectroscopy of the neutrals and photoelectron spectroscopy of their anions. Both of the spectroscopic analyses reveal that most of the Ln atoms preferably take +3 oxidation states, while Eu atoms alone assume +2 oxidation states, and that C(60) accepts up to twelve donated electrons in Ln(n)C(60). An additional photoionization examination of the oxygen atom mixing into the Ln(n)C(60) clusters demonstrated that each oxygen atom reduces two electrons from C(60). This result implies that the number of accepted electrons in C(60) can be varied by a suitable choice of the number of Ln atoms and O atoms.     

Syntheses and Crystal Structures of Ruthenium Complexes of 1,4,8,11-Tetraazacyclotetradecane, Tris(2-aminoethyl)amine (tren), and Bis(2-aminoethyl)(iminomethyl)amine. A Microporous Layered Structure Consisting of {[K(tren)](2)[RuCl(6)]}(n)()(n)()(-) and {(H(5)O(2))(4)[RuCl(6)]}(n)()(n)()(+)

The second method for the synthesis of cis-[Ru(III)Cl(2)(cyclam)]Cl (1) (cyclam = 1,4,8,11-tetraazacyclotetradecane), with use of cis-Ru(II)Cl(2)(DMSO)(4) (DMSO = dimethyl sulfoxide) as a starting complex, is reported together with the synthesis of [Ru(II)(cyclam)(bpy)](BF(4))(2).H(2)O (2) (bpy = 2,2'-bipyridine) from 1. The syntheses of Ru complexes of tris(2-aminoethyl)amine (tren) are also reported. A reaction between K(3)[Ru(III)(ox)(3)] (ox = oxalate) and tren affords fac-[Ru(III)Cl(3)(trenH)]Cl.(1)/(2)H(2)O (3) (trenH = bis(2-aminoethyl)(2-ammonioethyl)amine = monoprotonated tren) and (H(5)O(2))(2)[K(tren)][Ru(III)Cl(6)] (4) as major products and gives fac-[Ru(III)Cl(ox)(trenH)]Cl.(3)/(2)H(2)O (5) in very low reproducibility. A reaction between 3 and bpy affords [Ru(II)(baia)(bpy)](BF(4))(2) (6) (baia = bis(2-aminoethyl)(iminomethyl)amine), in which tren undergoes a selective dehydrogenation into baia. The crystal structures of 2-6 have been determined by X-ray diffraction, and their structural features are discussed in detail. Crystallographic data are as follows: 2, RuF(8)ON(6)C(20)B(2)H(34), monoclinic, space group P2(1)/c with a = 12.448(3) ?, b = 13.200(7) ?, c = 17.973(4) ?, beta = 104.28(2) degrees, V = 2862(2) ?(3), and Z = 4; 3, RuCl(4)O(0.5)N(4)C(6)H(20), monoclinic, space group P2(1)/a with a = 13.731(2) ?, b = 14.319(4) ?, c = 13.949(2) ?, beta = 90.77(1) degrees, V = 2742(1) ?(3), and Z = 8; 4, RuKCl(6)O(4)N(4)C(6)H(28), trigonal, space group R&thremacr; with a = 10.254(4), c = 35.03(1) ?, V = 3190(2) ?(3), and Z = 6; 5, RuCl(2)O(5.5)N(4)C(8)H(22), triclinic, space group P&onemacr; with a = 10.336(2) ?, b = 14.835(2) ?, c = 10.234(1) ?, alpha = 90.28(1) degrees, beta = 90.99(1) degrees, gamma = 92.07(1) degrees, V = 1567.9(4) ?(3), and Z = 4; 6, RuF(8)N(6)C(16)B(2)H(24), monoclinic, space group P2(1)/c, a = 10.779(2) ?, b = 14.416(3) ?, c = 14.190(2) ?, beta = 93.75(2) degrees, V = 2200.3(7) ?(3), and Z = 4. Compound 4 possesses a very unique layered structure made up of both anionic and cationic slabs, {[K(tren)](2)[Ru(III)Cl(6)]}(n)()(n)()(-) and {(H(5)O(2))(4)[Ru(III)Cl(6)]}(n)()(n)()(+) (n = infinity), in which both sheets {[K(tren)](2)}(n)()(2)(n)()(+) and {(H(5)O(2))(4)}(n)()(4)(n)()(+) offer cylindrical pores that are occupied with the [Ru(III)Cl(6)](3)(-) anions. The presence of a C=N double bond of baia in 6 is judged from the C-N distance of 1.28(2) ?. It is suggested that the structural restraint enhanced by the attachment of alkylene chelates at the nitrogen donors of amines results in either the mislocation or misdirection of the donors, leading to the elongation of the Ru-N(amine) distances and to the weakening of their trans influence. Such structural strain is also discussed as related to the spectroscopic and electrochemical properties of the cis-[Ru(II)L(4)(bpy)](2+) complexes (L(4) = (NH(3))(4), (ethylenediamine)(2), and cyclam).     

Dehydrogenation versus oxygenation in two-electron and four-electron reduction of dioxygen by 9-alkyl-10-methyl-9,10-dihydroacridines catalyzed by monomeric cobalt porphyrins and cofacial dicobalt porphyrins in the presence of perchloric acid

Dehydrogenation of 10-methyl-9,10-dihydroacridine (AcrH(2)) by dioxygen (O(2)) proceeds efficiently, accompanied by the two-electron and four-electron reduction of O(2) to produce H(2)O(2) and H(2)O, which are effectively catalyzed by monomeric cobalt porphyrins and cofacial dicobalt porphyrins in the presence of perchloric acid (HClO(4)) in acetonitrile (MeCN) and benzonitrile (PhCN), respectively. The cobalt porphyrin catalyzed two-electron reduction of O(2) also occurs efficiently by 9-alkyl-10-methyl-9,10-dihydroacridines (AcrHR; R = Me, Et, and CH(2)COOEt) to yield 9-alkyl-10-methylacridinium ion (AcrR+) and H(2)O(2). In the case of R = Bu(t) and CMe(2)COOMe, however, the catalytic two-electron and four-electron reduction of O(2) by AcrHR results in oxygenation of the alkyl group of AcrHR rather than dehydrogenation to yield 10-methylacridinium ion (AcrH+) and the oxygenated products of the alkyl groups, i.e., the corresponding hydroperoxides (ROOH) and the alcohol (ROH), respectively. The catalytic mechanisms of the dehydrogenation vs the oxygenation of AcrHR in the two-electron and four-electron reduction of O(2), catalyzed by monomeric cobalt porphyrins and cofacial dicobalt porphyrins, respectively, are discussed in relation to the C(9)-H or C(9)-C bond cleavage of AcrHR radical cations produced in the electron-transfer oxidation of AcrHR.     

Studies on the metabolism of gomisin A (TJN-101). II. Structure determination of biliary and urinary metabolites in rat

After oral administration of gomisin A (1) to rats, the bile and urine were collected and treated with beta-glucuronidase and arylsulfatase. Seven metabolites, met B (2), met A-III (3), met E (4), met D (5), met F (6), met G (7), and met H (8) were isolated from the bile treated with the enzymes. Eight metabolites 2-8, and met A-II (9) were isolated from the urine treated with the enzymes. A major metabolite 2, and two minor metabolites 3 and 9 were identified as met B, met A-III, and met A-II, respectively, which are oxidative products of 1 formed by rat liver S9 mix. The structures of five new metabolites 4-7, and 8 were determined on the basis of chemical and spectral studies.