Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays

Histone methylation is an epigenetic mark essential for gene regulation and development. We introduce peptide SPOT synthesis to study sequence specificity of the Dim-5 histone-3 lysine-9 methyltransferase. Dim-5 recognizes R8-G12 of the H3 tail with T11 and G12 being the most important specificity determinants. Exchange of H3 tail residue S10 and T11 by E strongly reduced methylation by Dim-5, suggesting that phosphorylation of S10 or T11 may regulate the activity of Dim-5. In the Dim-5/peptide structure, E227 interacts with H3R8 and D209 with H3-S10. Mutations of E227 or D209 caused predictable changes in the substrate preference, illustrating that peptide recognition of histone methyltransferases can be altered by protein design. Comparative analyses of peptide arrays with wild-type and mutant enzymes, therefore, are well suited to investigate the target specificity of protein methyltransferases and study epigenetic crosstalk.     

Modulating Electronic Coupling Using O- and S-donor Linkers

Structures of compounds having two dimolybdenum units Mo2(DAniF)3+ (DAniF = N,N'-di-p-anisylformamidinate) connected by unsubstituted oxamidate (1) and dithiooxamidate (2) linkers are isomorphous, and the cores of the molecules are planar because of two intramolecular hydrogen bonds within the linkers. Molecular mechanics calculations show a barrier of rotation along the C-C bond of approximately 10 kcal x mol(-1), which suggests that planar conformations are also expected in solution. Changing the two oxygen atoms in the linker of 1 to sulfur atoms results in a significant enhancement of the electronic coupling between the dimetal units (Delta(E1/2) = 204 mV for 1 and 407 mV for 2). The electronic spectrum of 2 shows an intense low energy (600 nm) metal-to-ligand charge transfer (MLCT) band, whereas that for 1 shows only a weak absorption band at 460 nm. DFT calculations on models 1' and 2', in which the anisyl groups were replaced by hydrogen atoms, show that the energy of the pi* orbital of the linker is much lower for 2'. This allows dpi-ddelta interactions from the electrons in the delta orbitals of the Mo2 unit to the sulfur atom that in turn facilitates an electron hopping pathway.     

Studies on the synthesis of (+/-)-stenine: a combined intramolecular [4 + 2]-cycloaddition/rearrangement cascade

Several cyclic 2-(methylthio)-5-amidofurans containing tethered unsaturation were prepared via the reaction of dimethyl(methylthio)sulfonium tetrafluoroborate (DMSTF) with beta-alkoxy-gamma-dithiane lactams. Thermolysis of these furans resulted in an intramolecular Diels-Alder reaction (IMDAF). The resulting oxa-bridge cycloadducts underwent a subsequent 1,2-methylthio shift to form tricyclic lactams in high yield. Furan 9, annealed to an azepine ring, underwent the IMDAF reaction at or below room temperature. Conformational effects imposed by the placement of a carbonyl group within the tether, combined with a rotational bias about the C(2)-N bond, enhances the rate of the IMDAF reaction of the seven-ring system so that it occurs readily at 25 degrees C. The feasibility of using the cascade sequence in the context of a total synthesis of the Stemona alkaloid (+/-)-stenine was explored. The eventual synthesis of (+/-)-stenine was carried out by an intramolecular Diels-Alder reaction of a 2-amido-5-methylthio-substituted furan containing a trans-pent-3-enoic acid methyl ester side chain in order to create the desired azepinoindole skeleton. This was followed by a series of reductions to set the syn-anti stereochemical relationship at the incipient ring fusion sites present in stenine. All six stereocenters at the azepinoindole core were derived in high stereoselectivity from the functionality present in the rearranged cycloadduct 10. Compound 10 was converted to stenine in 11 additional steps via a sequence that features a Crabtree's-catalyst directed hydrogenation, iodolactonization, and a Keck allylation.     

Efficient construction of the oxatricyclo[6.3.1.0(0,0)]dodecane core of komaroviquinone using a cyclization/cycloaddition cascade of a rhodium carbenoid intermediate

The rhodium(II)-catalyzed cyclization/cycloaddition cascade of a o-carbomethoxyaryl diazo dione is described as a potential route to the oxatricyclo[6.3.1.0(0,0)]dodecane substructure of the icetexane diterpene komaroviquinone. The initially formed carbonyl ylide dipole prefers to cyclize to an epoxide at 25 degrees C but can be induced to undergo cycloaddition across the tethered pi-bond at higher temperatures. [reaction: see text]     

Physisorption and Chemisorption on Silver Clusters

Adsorption and coadsorption studies on free silver clusters show that nitrogen physisorbs like rare gases, whereas oxygen chemisorbs with similarities and differences to bulk silver surfaces. Silver nanoparticles activate, or even dissociate adsorbed oxygen molecules. The global electron configurations of the adsorbent and adsorbate dominate the stability at small clusters. This is more important than geometry and site effects. Due to electronic shell effects and electron pairing, the activation of oxygen strongly varies with size. At more than 40 free electrons in the complex, such quantum effects start to blur. The size dependence becomes smoother and general trends govern the reactivity, which is driven by the interaction between the charge state of the nanoparticle and the charge transfer of the reaction.     

Tradition- and science-based quality control of Chinese medicines--introducing the Phyto-True system

The current QC practice of quantifying presumed active chemicals or arbitrarily selected chemical markers is of doubtful value in assessing multicomponent complex traditional Chinese medicines (CMs) and often leads to an inconsistent or irreproducible research and clinical outcome. Consequently, the first and most important step in the QC of CMs (or other botanical medicines) whose exact active chemical components are unknown is to use analytical techniques that can comprehensively define the totality of the components/attributes making up their identity and quality. One of the most versatile techniques is HPTLC. Using HPTLC, along with other simple techniques such as FTIR spectroscopy and UV-Vis spectroscopy combined with complementary gene expression profiling, we have been able to correctly identify CM materials, detect adulterants, and differentiate closely related materials and botanical species. Our research has resulted in the introduction of the concept and specimens of Phyto-True Reference Material (PTRM), aka Representative Botanical Reference/Research Material (RBRM), now commercially available, and a novel patent-pending technology (Phyto-True system) that can serve as a starting point for the meaningful QC of traditional CMs so far not possible for these complex materials. Examples will be highlighted to demonstrate this new concept.     

Excited state dynamics of metastable phthalocyanine-tetrasulfonate tetra-anions probed by pump/probe photoelectron spectroscopy

Femtosecond time-resolved pump-probe photoelectron spectroscopy was used to study elementary relaxation processes occurring in isolated phthalocyanine-tetrasulfonate tetra-anions ([MPc(SO3)4]4-, M=Cu,Ni, and "free-base" [H2Pc(SO3)4]4-) following Q band excitation by one-photon absorption at 775 nm. Whereas the Cu and Ni systems decay rapidly by means of internal conversion without electron loss, the free-base phthalocyanine primarily undergoes excited state tunneling electron emission. This reflects less efficient coupling to lower lying states within the corresponding spin manifold. Results are interpreted in terms of (time-dependent) density functional theory calculations of ground and electronically excited states and kinetically modeled to yield the associated rates.     

Photodissociation dynamics of gaseous CpCo(CO)2 and ligand exchange reactions of CpCoH2 with C3H4, C3H6, and NH3

The photodissociation dynamics of CpCo(CO)(2) was studied in a molecular beam using photofragment translational energy spectroscopy with 157 nm photoionization detection of the metallic products. At 532 and 355 nm excitation, the dominant one-photon channel involved loss of a single CO ligand producing CpCoCO. The product angular distributions were isotropic, and a large fraction of excess energy appeared as product vibrational excitation. Production of CpCO + 2CO resulted from two-photon absorption processes. The two-photon dissociation of mixtures containing CpCo(CO)(2) and H(2) at the orifice of a pulsed nozzle was used to produce a novel 16-electron unsaturated species, CpCoH(2). Transition metal ligand exchange reactions, CpCoH(2) + L → CpCoL + H(2) (L = propyne, propene, or ammonia), were studied under single-collision conditions for the first time. In all cases, ligand exchange occurred via 18-electron association complexes with lifetimes comparable to their rotational periods. Although ligand exchange reactions were not detected from CpCoH(2) collisions with methane or propane (L = CH(4) or C(3)H(8)), a molecular beam containing CpCoCH(4) was produced by photolysis of mixtures containing CpCo(CO)(2) and CH(4).     

Degenerate molecular shuttles with flexible and rigid spacers

The preparation and dynamic behavior of degenerate rotaxane molecular shuttles are described in which a benzylic amide macrocycle moves back and forth between two naphthalimide-glycine units along a diphenylethyne spacer or an aliphatic spacer consisting of a C(9), C(12), or C(26) alkyl chain. Subtle differences in the (1)H NMR spectra of the rotaxanes can be related to the presence of conformers in which the macrocycle interacts simultaneously with both glycines, especially in the case of the C(9) spacer. The kinetic data of the shuttling behavior in the C(26) rotaxane were obtained from dynamic NMR spectroscopy. The Eyring activation parameters were found to be ΔH(?) = 10 ± 1 kcal mol(-1), ΔS(?) = -6.5 ± 2.0 cal mol(-1) K(-1), ΔG(?)(298) = 11.9 ± 0.2 kcal mol(-1). For the systems with the shorter spacers, the shuttling rates were higher. Also in the diphenylethyne, rotaxane shuttling is rapid on the NMR time scale, indicating that the rigid unit does not impose a large barrier to the translocation of the macrocycle.     

Quantitative Analysis of Long Chain Fatty Acids Present in a Type I Kerogen Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Compared with BF3/MeOH Methylation/GC-FID

Long chain fatty acids (LCFAs) are present in various natural samples and are easily detectable using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) in negative ion mode. The capability of the ESI-FT-ICR-MS for quantifying LCFAs was evaluated by performing a standard addition followed by an internal standard methodology to several kerogen extracts using n-C₂₀ fatty acid as standard. As the concentration of the standard increased, the magnitude of its peak (m/z 311.29525) increased linearly but with two separate slopes, leaving the entire mass spectra relatively unchanged, which shows evidence of reproducibility. Response factors of other LCFAs are obtained using a standard addition approach. We employed five LCFA standards (n-C₁₅, n-C₁₉, n-C₂₄, n-C₂₆, and n-C₃₀) with different carbon numbers. This allowed us to determine the response factor of all fatty acids (with carbon number between 15 and 30) by plotting the slope of each standard versus its carbon number. With the observed response factors and use of the internal standard, the concentrations of LCFAs in four kerogen extracts were measured by ESI-FT-ICR-MS and compared with those from GC-FID. The carbon number distribution obtained by ESI-FT-ICR-MS matched well the GC-FID distribution (5%–50%) with the exception of C₁₆ and C₁₈, considering that ESI-FT-ICR-MS does not differentiate between normal and branched LCFAs, whereas GC-FID does. This allows one to quantitatively compare samples with a relatively similar matrix for specific compounds such as LCFAs with no need of time-consuming derivatization procedures. Moreover, the calibration can be extended to higher carbon numbers with ESI-FT-ICR-MS, beyond the capabilities of GC/MS.