Unusual heme-histidine bond in the active site of a chaperone

The heme chaperone CcmE is essential for the delivery of heme to c-type cytochromes. It forms an unusual transient, yet covalent, bond between an essential histidine, H130, and heme. We report on the discovery of the chemical structure of this bond solved by NMR, where the heme vinyl is cross-linked at the beta carbon to the Ndelta1 of H130. As this type of heme linkage has not been described previously in any cytochrome or hemoprotein, it represents a novel type of heme-histidine complex.     

Avoiding negative populations in explicit Poisson tau-leaping

The explicit tau-leaping procedure attempts to speed up the stochastic simulation of a chemically reacting system by approximating the number of firings of each reaction channel during a chosen time increment tau as a Poisson random variable. Since the Poisson random variable can have arbitrarily large sample values, there is always the possibility that this procedure will cause one or more reaction channels to fire so many times during tau that the population of some reactant species will be driven negative. Two recent papers have shown how that unacceptable occurrence can be avoided by replacing the Poisson random variables with binomial random variables, whose values are naturally bounded. This paper describes a modified Poisson tau-leaping procedure that also avoids negative populations, but is easier to implement than the binomial procedure. The new Poisson procedure also introduces a second control parameter, whose value essentially dials the procedure from the original Poisson tau-leaping at one extreme to the exact stochastic simulation algorithm at the other; therefore, the modified Poisson procedure will generally be more accurate than the original Poisson procedure.     

Mass spectrometrically detected directly coupled high performance liquid chromatography/nuclear magnetic resonance spectroscopy/mass spectrometry for the identification of xenobiotic metabolites in maize plants

Reconstructed ion chromatograms have been used to identify relevant high performance liquid chromatography (HPLC) peaks in a directly coupled high performance liquid chromatography/nuclear magnetic resonance spectroscopy/mass spectrometry (HPLC/NMR/MS) experiment. This has been applied to a study of the metabolism of a model compound, 5-nitropyridone (2-hydroxy-5-nitropyridine), in maize plants grown hydroponically. By monitoring the on-flow reconstructed ion chromatogram corresponding to the 5-nitropyridone fragment at m/z 143, and additional molecular ions corresponding to metabolites identified as products from similar compounds, relevant peaks were identified rapidly for subsequent stopped-flow 1H NMR spectroscopic analysis. The combination of coupled HPLC/NMR/MS enabled the direct identification of three metabolites, namely the N-glucoside, N-malonylglucoside, and O-malonylglucoside. This work demonstrates the power of HPLC/NMR/MS for the structural elucidation of xenobiotic metabolites in complex biological matrices (such as plant material) with minimal sample preparation. In particular, using mass spectrometry for the initial identification of relevant HPLC peaks allows the analysis of complex samples without the necessity for other spectroscopic markers, such as 19F NMR signal for fluorinated compounds or UV spectroscopy for molecules with strong UV chromophores.     

Separation of Trp-Arg and Arg-Trp using G-quartet-forming DNA oligonucleotides in open-tubular capillary electrochromatography

DNA oligonucleotides that form intramolecular G-quartet structures were investigated as stationary phase reagents for separation of mixtures of the isomeric dipeptides Trp-Arg and Arg-Trp in open-tubular capillary electrochromatography (OTCEC). The oligonucleotides included a thrombin-binding aptamer that forms a biplanar G-quartet structure and an oligonucleotide that forms a 4-plane G-quartet structure. Fluorescence, circular dichroism and UV-visible absorbance spectroscopies were used in batch solution studies to indicate interactions between the dipeptides and the biplanar G-quartet structure. Results for OTCEC separations were compared with results obtained for capillary zone electrophoresis separations on a bare capillary. Temperature studies suggest that resolution is improved when the G-quartet structure is partially destabilized, but control experiments in which potassium chloride was not included in the mobile phase indicate that the G-quartet structure nevertheless plays a role in the separations.     

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.     

Synthesis and structural characterization of [SiMe2(C5H4)2][(C5Me5) Zr(μ-S)]2. a dinuclear zirconocenophane complex with a skewed dimethylsilyl-bridged bis(cyclopentadienyl) ligand

The reaction of [SiMe₂(C₅H₄)₂][(C₅Me₅)ZrMe₂]₂ with H₂S at 110°C proceeds with the formation of [SiMe₂(C₅H₄)₂][(C₅Me₅)Zr(-S)]₂]₂. The molecular structure of this dinuclear zirconocenophane compound features a non-planar four-membered Zr₂(-S)_{2 2} ring with two symmetrically-bridging sulfido groups. The bridging dimethylsilyl-bridged bis(cyclopentadienyl) ligand adopts a skewed orientation to accommodate the long Zr ... Zr separation of 3.611(1) Å. This compound crystallizes in the centrosymmetric space group P1 with refined lattice parameters ofa = 10.905(1) Å,b = 10.939(2) Å,c = 14.621(2) Å, = 106.32(1)°, = 91.25(1)°, = 111.25(1)°,V = 1545.1(8) ų, _calc. = 1.512g/cm³,Z=2. Full-matrix refinement converged with final discrepancy indices of R(F _o = 0.045 andR(F _o) = 0.079 with GOF= 1.60 for 4403 data withF _o > 3(F _o).This paper is dedicated to Professor Larry Dahl, a valued friend and mentor, on the occasion of his 65th birthday and in recognition of his significant fundamental contributions to the field of metal cluster chemistry. May the Goddess Fortuna continue to bring distinction and honor to him and his research endeavors.     

ABSORPTION SPECTRAL SHIFTS OF CAROTENOIDS RELATED TO MEDIUM POLARIZABILITY

Abstract–Solvent induced absorption spectral shifts of the electronic transition from ground 1 A_g state to the excited 1B_u state in carotenoids have been studied. It is shown that the shift depends only on dispersion interactions in non-polar solvents. In polar media there is just a small extra contribution to the red-shift, due to other forms of interactions. The spectral shifts are well described by the theory, which expresses the shift relative to the gas phase value, as a function of solvent polarizability. The main conclusion is that the dominating mechanism behind the large red-shifted absorbance of carotenoids in the proteinacous environment, in vivo, is the mutual polarizability interactions between the carotenoids and the surrounding medium. The solution-phase values of the dipole moments of the lA_g to 1B_u transitions and the differences of isotropic polarizability between 1B_u and lA_g states of carotenoids in non-polar solvents are calculated and found to be around 13 D and 360 ų respectively. From the great overlap of absorption spectra between carotenoids in quinoline and carotenoids in vivo in purple bacterial antenna complexes, it can be expected that the carotenoids are surrounded by several aromatic amino acids in vivo. Comparisons have been done between the exicted states in carotenoids and in linear conjugated polyenes.     

A new ligand system based on a bipyridine-functionalized calix[4]arene backbone leading to mono- and bimetallic complexes

The synthesis of a new ligand system for mono- and bimetallic complexes based on a calixarene is described. Ligand BBPC (3, bis(bipyridine)-calix[4]arene) is obtained in three steps in 40% overall yield by first brominating one of the methyl groups of the 4,4'-dimethyl-2,2'-bipyridine in two steps and subsequently reacting it with p-tert-butylcalix[4]arene under basic conditions. Reaction of BBPC (3) with 2 equiv of [Rh(NBD)(2)]BF(4) or [Rh(NBD)(CH(3)CN)(2)]BF(4) (NBD = norbornadiene) produces the bimetallic compound BBPC[Rh(NBD)BF(4)](2) (4). Treatment of the ligand with PdCl(2)(CH(3)CN)(2) leads to the isolation of the bimetallic complex BBPC[PdCl(2)](2) (5). When the nickel precursor NiBr(2)(DME) (DME = dimethoxyethane) is reacted with BBPC, the bimetallic complex BBPC[NiBr(2)](2) (6) is isolated which, upon crystallization from methanol, gives the mononuclear bis(bipyridine) complex BBPC[NiBr(OMe)] (7). Full characterization includes X-ray structural studies of complexes 4, 5, and 7. The bimetallic compounds 4 and 5 show metal to metal distances of 4.334 A (for 4) and 3.224 A (for 5). For all three complexes, unique molecular packing arrangements were found, based on hydrophobic/hydrophilic interactions.     

Surface hydration and its effect on fluorinated SAM formation on SiO2 surfaces

Substrate hydration is demonstrated to be crucial to film quality during self-assembled (SA) film deposition of tridecafluoro-1,1,2,2,-tetrahydrooctyltrichlorosilane (FOTS) from the vapor phase. The surface hydration was studied by thermogravimetric analysis, and a model was developed to predict the conditions necessary to desorb all of the water adsorbed on a fused silica surface without significantly altering the concentration of the surface hydroxyl groups. The nature of the SA film was investigated as a function of the degree of rehydration of the dehydrated silica surface. The wettability and microstructure of the SA films were examined by water contact angle, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy. There is an optimum degree of substrate hydration, on the order of 1-1.2 monolayers of adsorbed water, required to produce a dense, durable and uniform FOTS film with high water repellency and a smooth surface.     

Nucleophilic de-coordination and electrophilic regeneration of "hemilabile" pincer-type complexes: formation of anionic dialkyl, diaryl, and dihydride Pt(II) complexes bearing no stabilizing pi-acceptors

Novel anionic dialkyl, diaryl, and dihydride platinum(II) complexes based on the new "long-arm" hemilabile PCN-type ligand C6H4[CH2P(tBu)2](CH2)2N(CH3)2 with the general formula Li+[Pt(PCN)(R)2]- (R=Me (4), Ph (6) and H (9)) were prepared by reaction of [Pt(PCN)(R)] complexes (obtained from the corresponding chlorides) with an equivalent of RLi, as a result of the opening of the chelate ring. Alkylating agents based on other metals produce less stable products. These anionic d8 complexes are thermally stable although they bear no stabilizing pi acceptors. They were characterized by 1H, 31P[1H], 13C, and 7Li NMR spectroscopy; complex 9 was also characterized by single crystal X-ray crystallography, showing that the Li+ ion is coordinated to the nitrogen atom of the open amine arm and to the hydride ligand (trans to the P atom) of a neighboring molecule (H--Li=2.15 A), resulting in a dimeric structure. Complexes 4 and 9 exhibit high nucleophilic reactivity, upon which the pincer complex is regenerated. Reaction of 4 with water, methyl iodide, and iodobenzene resulted in the neutral complex [Pt(PCN)(CH3)] (3) and methane, ethane, or toluene, respectively. Labeling studies indicate that the reaction proceeds by direct electrophilic attack on the metal center, rather than attack on the alkyl ligand. The anionic dihydride complex 9 reacted with water and methyl iodide to yield [Pt(PCN)(H)] (8) and H2 or methane, respectively.