C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI

We have examined the backbone dynamics of two alternating purine-pyrimidine dodecamers. One sequence consists of "pure" GC bases; the other one contains 5-methylcytosines. The effect of the methyl groups on the backbone substates BI/BII was investigated by means of molecular dynamics. The methylation influences, on one hand, the transition barrier between BI and BII and, on the other hand, the state of equilibrium. The kinetic consequences are an increase of the DeltaG of Gp5mC steps by 1.5 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol (compared with the nonmethylated DNA). Thus, the additive group differentiates between the two occurring dinucleotide steps and renders the phosphate of the 5-methylcytosine more rigid, as proposed by experimental studies. The thermodynamic consequences are an increase of the DeltaG of Gp5mC steps by 1.1 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol. The reason for this shift in equilibrium is still not completely clear on a molecular basis. But we can conclude that the indirect readout of DNA is influenced by methylation.     

Interelement correlations detectable in plant samples based on data from reference materials and highly accurate research samples

Summary A correlation analysis of 45 elements from various plant standard reference materials provided a number of highly correlated element pairs (r0.9) leading to the expectation of an interelement interaction. For the elements Fe³⁺, Al³⁺, Sc³⁺ and the lanthanides, these high correlations may be attributed to the similar ionic radius of the hydrated ions or the same charge. The highly correlated occurrence of some macroelements such as P and N reflects the close association of the two elements, particularly during protein biosynthesis. Of the alkali metals, K, and the alkaline earth metals Ca, Mg and, to some extent, also Sr display high correlations amongst themselves and with the macronutrients N and P. In correlating the transition elements with each other and with the micro- and macroelements, it was only possible to find a few high correlation coefficients; only the two element pairs Co/Mo and Cr/Co display high correlation coefficients. One of the reasons for this is probably the inaccuracy of the data material. It was not possible to confirm the highly negatively correlated element pairs reported in earlier work. It was not even possible to determine a clear negative trend for typical pairs of antagonists such as Al/Ca or Mn/Ca. The highest negative correlation was found for the B/Sb element pair at r=–0.75.     

Preparation of MxTa6−xS (M = V,Cr; x ≃ 1) A new columnar structure with interpenetrating metal icosahedra

The products of the high temperature reaction of Ta₂S with equimolar amounts of V and Cr, respectively, have been characterized by X-ray spectrometry and diffraction. The structures of the metal-rich compounds M_xTa_6?xS (M = V, Cr; x ? 1) have been determined from with single crystal X-ray intensities. The isotypic phases crystallize in the monoclinic space group C2/c four formula units per unit cell. The structure is interpreted as consisting of interpenetrating distorted metal icosahedra arranged to columns which in turn are connected to form layers via additional Ta? Ta interactions. Metal-sulphur and weaker metal–metal Bonds provide the linkage of the layers. The coordination about S is square antiprismatic. The structural relationship and fundamental distinctions between M_xTa_6?xS and Ta₆S are pointed out. Thermodynamic quantities are used to elucidate the various reaction products and differences between Ta_6?xV_xS and Cr_xTa_6?xS with respect to the phase widths.     

NONLINEAR POLARIZATION SPECTROSCOPY (FREQUENCY DOMAIN) STUDIES OF EXCITED STATE PROCESSES: THE B800–850ANTENNA OF RHODOBACTER SPHAEROIDES

Nonlinear polarization spectroscopy in the frequency domain allows rate constant determinations of fast electronic energy and phase relaxations together with characterization of the type of line broadening. Application of this method to the B850 component of the isolated B800–850antenna ofRhodobacter sphaeroides at room temperature shows that B850 is inhomogeneously broadened, with homogeneous widths between 30 and 200 cm^?1, depending on the spectral position of the subforms. The corresponding phase relaxation times are clearly in the subpicosecond range. There is also indication of an up-to-now unspecified1–5 ps energy relaxation channel per subunit.     

Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole

Summary Sterol 14α-demethylase (CYP51) is one of the known major targets for azole antifungals. Therapeutic side effects of these antifungals are based on interactions of the azoles with the human analogue enzyme. This study describes for the first time a comparison of a human CYP51 (HU-CYP51) homology model with a homology model of the fungal CYP51 of Candida albicans (CA-CYP51). Both models are constructed by using the crystal structure of Mycobacterium tuberculosis MT-CYP51 (PDB code: 1EA1).The binding mode of the azole ketoconazole is investigated in molecular dynamics simulations with the GROMACS force field. The usage of special parameters for the iron azole complex binding is necessary to obtain the correct complex geometry in the active site of the enzyme models. Based on the dynamics simulations it is possible to explain the enantioselectivity of the human enzyme and also to predict the binding mode of the isomers of ketoconazole in the active site of the fungal model.     

Characterization of (1)H-(1)H distances in a uniformly (2)H,(15)N-labeled SH3 domain by MAS solid-state NMR spectroscopy (section sign)

In this communication, we demonstrate the feasibility of obtaining long-range (1)H-(1)H distance information by MAS solid-state NMR for a microcrystalline, uniformly (2)H,(15)N-labeled sample of a SH3 domain of chicken alpha-spectrin. The experiments yield NOESY-type spectra and rely on the favorable dispersion of the (15)N chemical shifts of the protein backbone. Perdeuteration of nonexchangeable sites is employed to simplify proton spin systems and to obtain multiple structural information. Two mixing schemes, (1)H-(1)H double quantum filtered Post-C7 and (1)H spin diffusion, are implemented to obtain quantitative (1)H-(1)H distance information. Post-C7 and spin diffusion cross-peak buildup rates are discussed for initial-rate fitting and in the framework of n = 0 rotational resonance (rotor driven spin diffusion), respectively. Different deuteration schemes were tested to find conditions where short-range (1)H-(1)H interactions are truncated (e.g., between H(N) and H(alpha)), but long-range interactions are retained (e.g., between H(N) and H(N)).     

Inorganic chemical fingerprinting of the environment: “reference freshwater” — a useful tool for comparison and harmonization of analytical data in freshwater chemistry

An enormous amount of information about the state of the environment is being created in many programmes worldwide. Optimum use of this data requires, beside a high degree of quality control, a basis for comparability of single analytical values. This requirement is already fulfilled within the programmes, but more or less neglected between international programmes (Keune et al. [9]). The establishment of a synthetic “reference freshwater” can be a useful tool for the harmonization of environmental measurement. After normalization of the data measured in different inland water samples versus “reference freshwater”, a chemical fingerprinting of aquatic samples is now possible. In this paper, a fingerprint of Lake Baikal will be discussed and its comparability demonstrated.     

Crystal chemistry of the olivine-type LixFePO4 system () between 25 and 370 °C

The crystal chemistry of two initial mixtures of LiFePO₄ and heterosite FePO₄ (0.5LiFePO₄ + 0.5FePO₄; 0.75LiFePO₄ + 0.25FePO₄) was investigated through Neutron diffraction at 350 and 370 °C, respectively, and at room temperature after cooling. At 350 and 370 °C, Li_0.5FePO₄ and Li_0.75FePO₄ are refined as olivine-type single phases, in which Li⁺ ions are disordered. Significant anisotropic microstrains, within the (001)_Pmnb planes, occur, which may be accounted for by heterogeneous distance distributions within and between the [100]_Pmnb Li⁺ channels. On cooling back to room temperature, Li_0.5FePO₄ and Li_0.75FePO₄ single phases separate into mixtures of FePO₄ + Li_0.64FePO₄ and LiFePO₄ + Li_0.64FePO₄, respectively. The Li content of this metastable intermediate phase may correspond to the occupancy of 2 out of 3 Li sites within [100]_Pmnb Li⁺ channels. In Li_0,64FePO₄, average LiO bonds are longer than in LiFePO₄, whereas FeO bond lengths are shortened, due to a fraction of Fe(III). This may be at the origin of the metastability of such intermediate phase, and thus of the two-phase mechanism between LiFePO₄ and FePO₄.     

Selective generation and reactivity of 5'-adenosinyl and 2'-adenosinyl radicals

The reaction of hydrated electrons (e(-)(aq) with 8-bromoadenosine 7 has been investigated by radiolytic methods coupled with product studies. Pulse radiolysis revealed that one-electron reductive cleavage of the C-Br bond gives the C8 radical 8 followed by a fast radical translocation to the sugar moiety. The reaction is partitioned between C5' and C2' positions in a 60:40 ratio leading to 5'-adenosinyl radical 9 and 2'-adenosinyl radical 11. This radical translocation from C8 to different sites of the sugar moiety has also been addressed computationally by means of DFT B3LYP calculations. In addition, ketone 21 was prepared and photolyzed providing an independent generation of C2' radical 11. Both C5' and C2' radicals undergo unimolecular reactions. Radical 9 attacks adenine with a rate constant of 1.0 x 10(4) s(-1) and gives the aromatic aminyl radical 10, whereas C2' radical 11 liberates adenine with a rate constant of 1.1 x 10(5) s(-1).     

Reversible collapse of brushlike macromolecules in ethanol and water vapours as revealed by real-time scanning force microscopy

Environment-controlled scanning force microscopy allowed us to study adsorption and desorption of single poly(methacrylate)-graft-poly(n-butyl acrylate) brush molecules on mica in real time. The molecules transform reversibly from a two-dimensional, extended wormlike state to a compact globular state. The dynamics of the conformational transition was sufficiently slow in order to allow its observation by scanning force microscope in real time. The reversible transformation is effected by coadsorption of water or ethanol, the latter introduces the collapse. Adsorbing ethanol and water from the vapour atmosphere results in a change of the surface properties of mica, either favouring adsorption or desorption of the graft polymer. When the extended, tightly adsorbed poly(n-butyl acrylate) brush molecules are exposed to ethanol vapour, the macromolecules swell and contract to form compact globules. Exchanging the ethanol vapour to a humid atmosphere caused the molecules to extend again to a wormlike two-dimensional conformation. Coexistence of collapsed and extended strands within the same molecule indicates a single-molecule first-order transition in agreement with observations on Langmuir films previously reported.