Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

Reaction of nitric oxide at the beta-carbon of enamines. A new method of preparing compounds containing the diazeniumdiolate functional group

The reaction of nitric oxide (NO) with enamines has been investigated. Unlike previously reported reactions of NO as a free radical with alkenes, the electrophilic addition of NO to the beta-carbon of enamines results in the formation of compounds containing the diazeniumdiolate functional group (-[N(O)NO](-)). This reaction between NO and enamines has been shown to be quite general and a variety of enamine-derived diazeniumdiolates have been isolated and characterized. While enamines derived from aldehydes and ketones whose structures allow for sequential multiple electrophilic additions tended to undergo overreaction leading to unstable products, it has been shown that this complication may be overcome by suitable choice of reaction solvent. The products obtained may exist as zwitterionic iminium salts or as neutral species depending upon the structure of the parent enamine. The diazeniumdiolate derived from 1-(N-morpholino)cyclohexene is unique among the new compounds in that it spontaneously releases NO upon dissolution in buffered aqueous solution at pH 7.4 and 37 degrees C. While the total quantity of NO released by this material (ca. 7% of the theoretical 2 moles) is apparently limited by a competing reaction in which it hydrolyzes to an alpha-diazeniumdiolated carbonyl compound and the parent amine, this feature may prove to be of great value in the development of multiaction pharmaceuticals based upon this new type of NO-releasing compound. Reports of enzymatic (oxidative) release of NO from previously known carbon-bound diazeniumdiolates also suggest that analogues of these compounds may be useful as pharmaceutical agents. This new method of introducing the relatively rarely studied diazeniumdiolate functional group into organic compounds should lead to further research into its chemical and biological properties.     

Cymantrene radical cation family: spectral and structural characterization of the half-sandwich analogues of ferrocenium ion

The anodic one-electron oxidation of three members of the half-sandwich family of piano-stool compounds MnCp (gamma)(CO) 3, where Cp (gamma) is a generic cyclopentadienyl ligand, has been studied in a CH 2Cl 2/[NBu 4][TFAB] electrolyte (TFAB = [B(C6F5) 4] (-)). The long-sought 17 e (-) radical cation of the parent complex MnCp(CO) 3 (cymantrene, 1, E 1/2 = 0.92 V vs ferrocene) has been shown to be persistent in solutions that use weakly coordinating anions in place of more nucleophilic traditional electrolyte anions. Spectroscopically characterized for the first time, 1 (+) was shown to absorb in the visible (530 nm), near-IR (2066 nm), and IR (2118, 1934 cm (-1)) regions. It was ESR-active at low temperatures (g parallel = 2.213, g perpendicular = 2.079, A parallel (Mn) = 79.2 G, A perpendicular (Mn) = 50 G) and NMR active at room temperature (delta = 22.4 vs TMS). The radical cations of the Cp-functionalized analogues, Mn(eta (5)-C5H 4NH2)(CO) 3, 2, E 1/2 = 0.62 V, and MnCp*(CO) 3 (Cp*= eta (5)-C 5Me 5, 3), E 1/2 = 0.64 V, were generated electrochemically as well by the chemical oxidant [ReCp(CO) 3] (+). The structures of 2 (+) and 3 (+) were determined by X-ray crystallographic studies of their TFAB salts. Compared to the structures of the corresponding neutral compounds, the cations showed elongated Mn-C(O) bonds and shortened C-O bonds, displaying the effect of diminished metal-to-CO backbonding. The bond-length changes in the Mn(CO) 3 moiety were much larger in 3 (+) (avg changes, Mn-C(O) = + 0.142 A, C-O = -0.063 A) than in 2 (+) (avg changes, Mn-C(O) = + 0.006 A, C-O = -0.003 A). Although there were only minor changes in the metal-to-center ring distances upon oxidation of either 2 or 3, there was decidedly less bending of the C(N) atom out of the cyclopentadienyl plane in 2 (+) compared to 2. The optical, vibrational, and magnetic resonance spectra of radicals 2 (+) and 3 (+) were also observed. The spectral data argue for the SOMOs of the 17-electron species being largely located on the Mn(CO) 3 moiety, having 40-50% Mn d-orbital character, with the ground states of the radicals, most likely (2)A', lying close in energy (within about 6000 cm (-1)) to excited states that are responsible for their rapid electronic relaxations. The cymantrenyl moiety is proposed as an anodic redox tag (or label) having physical and chemical properties that are significantly different from those of its ferrocenyl analogue.     

Organolanthanide-based synthesis of 1,2,3-triazoles from nitriles and diazo compounds

The reaction of [(C5Me5)2Ln][(mu-Ph)2BPh2] complexes with the lithium salt of (trimethylsilyl)diazomethane, Li[Me3SiCN2], gave products formulated as the dimeric isocyanotrimethylsilyl amide complexes {(C5Me5)2Ln[mu-N(SiMe3)NC]}2 (Ln = Sm, 1; La, 2). Reactions of (C5Me5)2Sm and [(C5Me5)2Sm(mu-H)]2 with Me3SiCHN2 also form 1. Complexes 1 and 2 react with Me3CCN to form the 1,2,3-triazolato complexes (C5Me5)2Ln(NCCMe3)[NNC(SiMe3)C(CMe3)N] (Ln = Sm, 3; La, 4). Complex 2 reacts with Me3SiN3 to make the isocyanide ligated azide complex {(C5Me5)2La[CNN(SiMe3)2](mu-N3)}3, 5.     

The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy

Many proteins involved in signal transduction are equipped with covalently attached lipid chains providing a hydrophobic anchor targeting these molecules to membranes. Despite the considerable biological significance of this membrane binding mechanism for 5-10% of all cellular proteins, to date very little is known about structural and dynamical features of lipidated membrane binding domains. Here we report the first comprehensive study of the molecular dynamics of the C-terminus of membrane-associated full-length lipidated Ras protein determined by solid-state NMR. Fully functional lipid-modified N-Ras protein was obtained by chemical-biological synthesis ligating the expressed water soluble N-terminus with a chemically synthesized (2)H or (13)C labeled lipidated heptapeptide. Dynamical parameters for the lipid chain modification at Cys 181 were determined from static (2)H NMR order parameter and relaxation measurements. Order parameters describing the amplitude of motion in the protein backbone and the side chain were determined from site-specific measurements of (1)H-(13)C dipolar couplings for all seven amino acids in the membrane anchor of Ras. Finally, the correlation times of motion were determined from temperature dependent relaxation time measurements and analyzed using a modified Lipari Szabo approach. Overall, the C-terminus of Ras shows a versatile dynamics with segmental fluctuations and axially symmetric overall motions on the membrane surface. In particular, the lipid chain modifications are highly flexible in the membrane.     

Magnesium amido N-heterocyclic carbene complexes

Magnesium dications bind strongly to a tridentate anionic dicarbene ligand L = [N{CH(2)CH(2)(CNCHCHNMes)}(2)] forming dinuclear and trinuclear Mg complexes with some particularly short Mg-C bonds. Treatment of the proligand H(4)LCl(3) with three equivalents of methyl magnesium chloride or benzyl magnesium chloride affords Mg(3)(HL)Cl(6) in high yield. A suspension of in thf was heated to 80 degrees C for 2 h to afford Mg(2)(L)Cl(3), consistent with the loss of one equivalent of MgCl(2), and the deprotonation of the remaining acidic NH, lost as HCl gas. Treatment of Mg(3)(HL)Cl(6) with one equivalent of KC(8) results in deprotonation of the ligand amine NH to afford Mg(3)(L)Cl(5); treatment with a second equivalent forms the radical anion of the complex, K[Mg(3)(L)Cl(5)], which decomposes upon storage, precluding its structural characterisation. The acidic NH proton of the ligand in Mg(3)(HL)Cl(6) can also be removed by deprotonation with Li{N(SiMe(3))(2)}; additional equivalents of which also exchange the magnesium-bound chlorides for silylamido ligands, affording Mg(2)(L)Cl(2)N' and Mg(2)(L)Cl(N')(2), which have both been characterised by single-crystal X-ray diffraction studies.     

Raman spectrocopic studies on the vibrational relaxation of CH3CN in different environments

Comparison of the frequencies and half-widths of v₁ in a variety of solvents shows that dispersion forces make a significant contribution to the effective intermolecular potential. Measurements of τ_v^?1 and [ω²] in the CH₃CN/CD₃OD/CCl₄ system demonstrates that long-range (hydrogen-bonding?) potentials significantly affect the relaxation rate.     

Theoretical Study of Small Water Clusters of Sulfur Dioxide

The intermolecular clusters of sulfur dioxide with water, SO2(H2O)n (n = 2～5), are studied by using B3LYP density functional theory and MP2 ab initio methods along with the large basis sets (6-311++G(d,p) and aug-cc-pVDZ). The equilibrium geometries, intermolecular binding energies, and anharmonic frequencies of the clusters are calculated and compared with those of pure water clusters and available experiments. SO2 tends to form cyclic hydrogen-bonded complexes with two or three water molecules. In the larger clusters, however, water molecules begin to retain the structure of pure water clusters and segregate from SO2. Infrared absorption assignments for the small clusters are discussed to resolve a possible incorrect assignment in a recent spectroscopic experiment on the clusters.     

Synthesis of α,α-disubstituted aryl amines by rhodium-catalyzed amination of tertiary allylic trichloroacetimidates

The rhodium-catalyzed regioselective amination of tertiary allylic trichloroacetimidates with unactivated aromatic amines is a direct and efficient approach to the preparation of α,α-disubstituted allylic aryl amines in good yield and with excellent regioselectivity. This method is applicable to a variety of unactivated primary and secondary amines and allows for the preparation of reverse prenylated indoles in two steps.