Assignments of carbon NMR resonances for microcrystalline ubiquitin

Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).     

Aziridination of γ,δ-dibromoethyl-2-pentenoate with primary amines: extension of the Gabriel-Cromwell reaction

Ethyl (E)-4,5-dibromo-2-pentenoate readily reacts with an assortment of primary amines in the presence of DBU to afford the corresponding conjugated aziridines in good to moderate yields. That the reaction is compatible with a nucleoside-derived amine suggests a broad scope of application.     

The peripheral benzodiazepine receptor in photodynamic therapy with the phthalocyanine photosensitizer Pc 4

The peripheral benzodiazepine receptor (PBR) is an 18 kDa protein of the outer mitochondrial membrane that interacts with the voltage-dependent anion channel and may participate in formation of the permeability transition pore. The physiological role of PBR is reflected in the high-affinity binding of endogenous ligands that are metabolites of both cholesterol and heme. Certain porphyrin precursors of heme can be photosensitizers for photodynamic therapy (PDT), which depends on visible light activation of porphyrin-related macrocycles. Because the apparent binding affinity of a series of porphyrin analogs for PBR paralleled their ability to photoinactivate cells, PBR has been proposed as the molecular target for porphyrin-derived photocytotoxicity. The phthalocyanine (Pc) photosensitizer Pc 4 accumulates in mitochondria and structurally resembles porphyrins. Therefore, we tested the relevance of PBR binding on Pc 4-PDT. Binding affinity was measured by competition with 3H-PK11195, a high-affinity ligand of PBR, for binding to rat kidney mitochondria (RKM) or intact Chinese hamster ovary (CHO) cells. To assess the binding of the Pc directly, we synthesized 14C-labeled Pc 4 and found that whereas Pc 4 was a competitive inhibitor of 3H-PK11195 binding to the PBR, PK11195 did not inhibit the binding of 14C-Pc 4 to RKM. Further, 14C-Pc 4 binding to RKM showed no evidence of saturation up to 10 microM. Finally, when Pc 4-loaded CHO cells were exposed to activating red light, apoptosis was induced; Pc 4-PDT was less effective in causing apoptosis in a companion cell line overexpressing the antiapoptotic protein Bcl-2. For both cell lines, PK11195 inhibited PDT-induced apoptosis; however, the inhibition was transient and did not extend to overall cell death, as determined by clonogenic assay. The results demonstrate (1) the presence of low-affinity binding sites for Pc 4 on PBR; (2) the presence of multiple binding sites for Pc 4 in RKM and CHO cells other than those that influence PK11195 binding; and (3) the ability of high supersaturating levels of PK11195 to transiently inhibit apoptosis initiated by Pc 4-PDT, with less influence on overall cell killing. We conclude that the binding of Pc 4 to PBR is less relevant to the photocytotoxicity of Pc 4-PDT than are other mitochondrial events, such as photodamage to Bcl-2 and that the observed inhibition of Pc 4-PDT-induced apoptosis by PK11195 likely occurs through a mechanism independent of PBR.     

Fragmentation of N-linked glycans with a matrix-assisted laser desorption/ionization ion trap time-of-flight mass spectrometer

N-Linked glycans were ionized from several matrices with a Shimadzu-Biotech AXIMA-QIT matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometer. [M+Na]+ ions were produced from all matrices and were accompanied by varying amounts of in-source fragmentation products. The least fragmentation was produced by 2,5-dihydroxybenzoic acid and the most by alpha-cyano-4-hydroxycinnamic acid and 6-aza-2-thiothymine. Sialic acid loss was extensive but could be prevented by formation of methyl esters. Fragmentation produced typical low-energy-type spectra dominated by ions formed by glycosidic cleavages. MS(n) spectra (n = 3 and 4) were used to probe the pathways leading to the major diagnostic ions. Thus, for example, an ion that was formed by loss of the core GlcNAc residues and the 3-antenna was confirmed as being formed by a B/Y rather than a C/Z mechanism. The proposed structures of several cross-ring cleavage ions were confirmed and it was shown that MS3 spectra could be obtained from as little as 10 fmol of glycan.     

Determination of the size and composition of multicomponent ethanol/water droplets by cavity-enhanced Raman scattering

Cavity-enhanced Raman scattering is used to determine the size and composition of multicomponent ethanol/water droplets in the concentration range 7.5–19% ethanol by volume. Under the experimental conditions presented here, the integrated CERS signal from ethanol shows an exponential increase with increase in ethanol concentration when compared with the integrated intensity of the water band. The calibration is shown to be invariant with particle size over the droplet radius range 20–35 μm. In addition to providing a method for determining particle size and composition, initial studies show that the evaporation dynamics of these multicomponent droplets can be probed by CERS.     

Imaging the quantum-state specific differential cross sections of HCl formed from reactions of chlorine atoms with methanol and dimethyl ether

Center-of-mass frame scattering angle distributions obtained directly from crossed molecular beam velocity map images are reported for HCl formed in different rotational levels of its vibrational ground state by reaction of Cl atoms with CH3OH and CH3OCH3. Products are observed to scatter over all angles, with peaks in the distribution in the forward and backward directions (theta = 0 and 180 degrees with respect to the relative velocity vectors of the Cl atoms). Products of both reactions exhibit differential cross sections that vary with the rotational quantum number of the HCl, with a greater propensity for forward scatter for J = 2, shifting to more pronounced backward scatter for J = 5. This trend is, however, more evident for reaction of dimethyl ether than for methanol. The mean fractions of the available energy channeled into product kinetic energy vary with scattering angle, but the angle-averaged fractions are, respectively, 0.37 and 0.42 for the methanol and dimethyl ether reactions. On average, 46% or more of the available energy of the reactions becomes internal energy of the radical co-product. Results are interpreted with the aid of computed energies of transition states and molecular complexes along the reaction pathways, and comparisons are drawn with recent measurements of the scattering distributions and energy release for reactions of Cl atoms with small alkanes.     

Mixed-metal cluster chemistry. 28. Core enlargement of tungsten-iridium clusters with alkynyl, ethyndiyl, and butadiyndiyl reagents

Reaction of [WIr3(mu-CO)3(CO)8(eta-C5Me5)] (1c) with [W(C[triple bond]CPh)(CO)3(eta-C5H5)] afforded the edge-bridged tetrahedral cluster [W2Ir3(mu4-eta2-C2Ph)(mu-CO)(CO)9(eta-C5H5)(eta-C5Me5)] (3) and the edge-bridged trigonal-bipyramidal cluster [W3Ir3(mu4-eta2-C2Ph)(mu-eta2-C=CHPh)(Cl)(CO)8(eta-C5Me5)(eta-C5H5)2] (4) in poor to fair yield. Cluster 3 forms by insertion of [W(C[triple bond]CPh)(CO)3(eta-C5H5)] into Ir-Ir and W-Ir bonds, accompanied by a change in coordination mode from a terminally bonded alkynyl to a mu4-eta2 alkynyl ligand. Cluster 4 contains an alkynyl ligand interacting with two iridium atoms and two tungsten atoms in a mu4-eta2 fashion, as well as a vinylidene ligand bridging a W-W bond. Reaction of [WIr3(CO)11(eta-C5H5)] (1a) or 1c with [(eta-C5H5)(CO)2 Ru(C[triple bond]C)Ru(CO)2(eta-C5H5)] afforded [Ru2WIr3(mu5-eta2-C2)(mu-CO)3(CO)7(eta-C5H5)2(eta-C5R5)] [R = H (5a), Me (5c)] in low yield, a structural study of 5a revealing a WIr3 butterfly core capped and spiked by Ru atoms; the diruthenium ethyndiyl precursor has undergone Ru-C scission, with insertion of the C2 unit into a W-Ir bond of the cluster precursor. Reaction of [W2Ir2(CO)10(eta-C5H5)2] with the diruthenium ethyndiyl reagent gave [RuW2Ir2{mu4-eta2-(C2C[triple bond]C)Ru(CO)2(eta-C5H5)}(mu-CO)2(CO)6(eta-C5H5)3] (6) in low yield, a structural study of 6 revealing a butterfly W2Ir2 unit capped by a Ru(eta-C5H5) group resulting from Ru-C scission; the terminal C2 of a new ruthenium-bound butadiyndiyl ligand has been inserted into the W-Ir bond. Reaction between 1a, [WIr3(CO)11(eta-C5H4Me)] (1b), or 1c and [(eta-C5H5)(CO)3W(C[triple bond]CC[triple bond]C)W(CO)3(eta-C5H5)] afforded [W2Ir3{mu4-eta2-(C2C[triple bond]C)W(CO)3(eta-C5H5)}(mu-CO)2(CO)2(eta-C5H5)(eta-C5R5)] [R = H (7a), Me (7c); R5 = H4Me (7b)] in good yield, a structural study of 7c revealing it to be a metallaethynyl analogue of 3.     

Metalloglycomics: a new perspective upon competitive metal-carbohydrate binding using EPR spectroscopy

Ternary complexes formed between calcium, the oxochromium(v) ion and N-acetylneuraminic (sialic) acid (naH(6)) of the form, Ca(ii)-oxoCr(v)-naH(6), have electronic structures and equilibrium distributions distinct from the binary oxoCr(v)-naH(6) analogues, as illustrated by electron paramagnetic resonance (EPR) spectroscopy.     

Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules

Evolutionary approaches are regularly used to isolate single molecules with desired activities from large populations of nucleic acids (approximately 10(15)). Several methods have also been developed to generate libraries of mRNA-encoded peptides and proteins for the in vitro selection of functional polypeptides. In principal, such mRNA encoding systems could be used with libraries of nonbiological polymers if the ribosome can be directed to polymerize tRNAs carrying unnatural amino acids. The fundamental problem is that current chemical aminoacylation systems cannot easily produce sufficient amounts of the numerous misacylated tRNAs required to synthesize a complex library of encoded polymers. Here, we show that bulk-aminoacylated tRNA can be transformed into N-monomethylated aminoacyl tRNA and translated. Because poly-N-methyl peptide backbones are refractory to proteases and are membrane permeable, our method provides an uncomplicated means of evolving novel drug candidates.     

Preparation of methyl (1R,2S,5S)- and (1S,2R,5R)-2-amino-5-tert-butyl-cyclopentane-1-carboxylates by parallel kinetic resolution of methyl (RS)-5-tert-butyl-cyclopentene-1-carboxylate

Comparison of the kinetic and parallel kinetic resolutions of methyl (RS)-5-tert-butyl-cyclopentene-1-carboxylate allows for the efficient synthesis of both (1R,2S,5S)- and (1S,2R,5R)-enantiomers of methyl 2-amino-5-tert-butyl-cyclopentane-1-carboxylate.