Methyl side-chain dynamics in proteins using selective enrichment with a single isotopomer

13C relaxation studies on side-chain methyl groups in proteins typically involve measurements on (13)CHD(2) isotopomers, where the (13)C relaxation mechanism is particularly straightforward in the presence of a single proton. While such isotopomers can be obtained in proteins overexpressed in bacteria by use of (13)C enriched and fractionally deuterated media, invariably all possible (2)H isotopomers are obtained. This results in a loss of both resolution and sensitivity, which becomes particularly severe for larger proteins. We describe an approach that overcomes this problem by chemical synthesis of amino acids containing a pure (13)CHD(2) isotopomer. We illustrate the benefits of this approach in (13)C side-chain relaxation measurements on the mouse major urinary protein selectively enriched with [gamma(1),gamma(2)-(13)C(2),alpha,beta,gamma(1),gamma(1),gamma(2),gamma(2)-(2)H(6)] valine. Relaxation measurements in the absence and presence of pyrazine-derived ligands suggest that valine side-chain dynamics do not contribute significantly to binding entropy.     

Stable polythiophene semiconductors incorporating thieno[2,3-b]thiophene

This work describes a new design methodology that allows the preparation of air stable, semiconducting thiophene polymers with high charge carrier mobilities. The incorporation of thieno[2,3-b]thiophene into a polythiophene backbone introduces cross-conjugated double bonds that disfavor full delocalization, leading to high ionization potential in comparison to a fully conjugated polythiophene, with no reduction in charge carrier mobility. The resulting solution processable polymers exhibit charge carrier mobilities up to 0.15 cm2/V s and on/off ratios greater than 105 when measured in air. Transistors exhibit lifetimes of several months in air with no encapsulation necessary.     

Effects of alkylation upon the proton affinities of nitrogen and oxygen bases

The protonation energies of alkylated derivatives of NH₃ and OH₂ are calculated at the Hartree–Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (～30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.     

Structural and Dynamic Study of SnCl4 · 2 Me2O and SnCl4 · 2 Me2Se Preliminary communication

The solid cis-SnCl₄ · 2Me₂O and trans-SnCl₄ · 2Me₂Se adducts have been synthesised and characterised by IR. and Raman spectroscopy. NMR. and vibrational spectroscopy show a fast cis-trans equilibrium for both complexes in solution in an inert solvent.     

Direct imaging of surface-enhanced Raman scattering in the near field

By using near-field scanning microscopy/spectroscopy, we show that surface-enhanced Raman scattering (SERS) of rhodamine 6G deposited on self-affine silver colloidal film is localized to small, down to less than 200 nm, portions of the film. The locus of the SERS signals ("hot spots") does not necessarily reside in special topographic elements such as interstices and between nanoparticles. The local SERS enhancement is estimated to be over 3 orders of magnitude higher compared to the far-field measurements. Near-field imaging of SERS directly validates the theory of the optical response of self-affine fractal objects.     

An investigation of the roles of surface aluminum and acid sites in the zeolite MCM-22

Ammonia adsorption studies reveal that the observed Lewis acidity in the zeolite MCM-22 is derived from at least two types of framework aluminum sites (AlF), that is, octahedral AlF and three-coordinate AlF. Comparative ammonia or trimethylphosphine (TMP) adsorption experiments with MCM-22 confirm that octahedral Al species gives rise to the signal at delta(iso) approximately 0 in the 27Al NMR spectrum; this is a superposition of two NMR signals from the different Al species on the water-reconstructed zeolite surface. A sharp resonance assigned to framework Al reversibly transforms on ammonia adsorption to delta(iso)27Al approximately 55 from tetrahedral AlF, while the broad peak is assigned to nonframework aluminum which results from hydrothermal treatment. This study also demonstrates the effectiveness of 27Al magic angle spinning (MAS) and multiple quantum (MQ) MAS NMR spectroscopy as a technique for the study of zeolite reactions.     

Structure-Based Calculations of the Optical Spectra of the LH2 Bacteriochlorophyll-Protein Complex from Rhodopseudomonas acidophila

Abstract— The molecular structure of the light-harvesting complex 2 (LH2) bacteriochlorophyll-protein antenna complex from the purple non-sulfur photosynthetic bacterium Rhodopseudomonas acidophila , strain 10050 provides the positions and orientations of the 27 bacteriochlorophyll (BChl) molecules in the complex. Our structure-based model calculations of the distinctive optical properties (absorption, CD, polarization) of LH2 in the near-infrared region use a point-monopole approximation to represent the BChl Q_y transition moment. The results of the calculations support the assignment of the ring of 18 closely coupled BChl to B850 (BChl absorbing at 850 nm) and the larger diameter, parallel ring of 9 weakly coupled BChl to B800. All of the significantly allowed transitions in the near infrared are calculated to be perpendicular to the C9 symmetry axis, in agreement with polarization studies of this membrane-associated complex. To match the absorption maxima of the B800 and B850 components using a relative permittivity (dielectric constant) of 2.1, we assign different site energies (12 500 and 12260 cm⁻¹, respectively) for the Q_y transitions of the respective BChl in their protein binding sites. Excitonic coupling is particularly strong among the set of B850 chromophores, with pairwise interaction energies nearly 300 cm between nearest neighbors, comparable with the experimental absorption bandwidths at room temperature. These strong interactions, for the full set of 18 B850 chromophores, result in an excitonic manifold that is 1200 cm⁻¹ wide. Some of the upper excitonic states should result in weak absorption and perhaps stronger CD features. These predictions from the calculations await experimental verification.     

Large-scale millisecond intersubunit dynamics in the B subunit homopentamer of the toxin derived from Escherichia coli O157

We report here solution NMR relaxation measurements that show millisecond time-scale intersubunit dynamics in the homopentameric B subunit (VTB) of the toxin derived from Escherichia coli O157. These data are consistent with interconversion between an axially symmetric form and a low-abundance ( approximately 10%, 45 degrees C) higher energy form. The higher energy state is depopulated on binding of a novel bivalent analogue (P(k) dimer) of the natural carbohydrate acceptor globotriaosylceramide. The isothermal titration calorimetry isotherm for the binding of P(k) dimer to VTB is consistent with a five-site sequential binding model which assumes that cooperative effects arise through communication only between neighboring binding sites. The resulting thermodynamic parameters (K(a1) = 114 +/- 2.2 M(-1), K(a2) = 283 +/- 4.5 M(-1), DeltaH(1) degrees = -116.3 +/- 0.55 kJ/mol, and DeltaH(2) degrees = -50.3 +/- 0.11 kJ/mol) indicate favorable entropic cooperativity that has not previously been observed in multivalent systems.     

Factors involved in the formation of amorphous and crystalline calcium carbonate: a study of an ascidian skeleton.

The majority of invertebrate skeletal tissues are composed of the most stable crystalline polymorphs of CaCO(3), calcite, and/or aragonite. Here we describe a composite skeletal tissue from an ascidian in which amorphous and crystalline calcium carbonate coexist in well-defined domains separated by an organic sheath. Each biogenic mineral phase has a characteristic Mg content (5.9 and 1.7 mol %, respectively) and concentration of intramineral proteins (0.05 and 0.01 wt %, respectively). Macromolecular extracts from various biogenic amorphous calcium carbonate (ACC) skeletons are typically glycoproteins, rich in glutamic acid and hydroxyamino acids. The proteins from the crystalline calcitic phases are aspartate-rich. Macromolecules extracted from biogenic ACC induced the formation of stabilized ACC and/or inhibited crystallization of calcite in vitro. The yield of the synthetic ACC was 15-20%. The presence of Mg facilitated the stabilization of ACC: the protein content in synthetic ACC was 0.12 wt % in the absence of Mg and 0.07 wt % in the presence of Mg (the Mg content in the precipitate was 8.5 mol %). In contrast, the macromolecules extracted from the calcitic layer induced the formation of calcite crystals with modified morphology similar to that expressed by the original biogenic calcite. We suggest that specialized macromolecules and magnesium ions may cooperate in the stabilization of intrinsically unstable amorphous calcium carbonate and in the formation of complex ACC/calcite tissues in vivo.     

Noncontact temperature measurement in microliter-sized volumes using fluorescent-labeled DNA oligomers

A new method of noncontact temperature measurement in microliter-sized volumes is demonstrated, based on the temperature sensitivity of the fluorescence lifetime of rhodamine-G when it is attached to a DNA oligomer. As temperature changes, the spacing between the fluorescent dye and a designed sequence of DNA bases is modulated by conformation changes of the DNA chain, and as a result the ability of dye molecules to fluoresce is also modulated according to differential quenching by bases on the DNA. In the system that we studied, the temperature sensitivity of the fluorescence lifetime was 36-42 ps/ degrees C depending on specific solution conditions. Although this strategy of temperature measurement is demonstrated using a specific sequence of DNA, it can also be generalized to a dye attached to any other intrinsic quencher of fluorescence whose conformation changes with temperature.