Quantitative analysis of two-dimensional gel-separated proteins using isotopically marked alkylating agents and matrix-assisted laser desorption/ionization mass spectrometry

We describe a simple approach for the relative quantification of individual proteins within a mixture. The method is based on the differential labelling of the mixtures by use of a commercially available acrylamide and deuterium-labelled [2,3,3'-d(3)]-acrylamide to alkylate proteins prior to two-dimensional (2-D) gel electrophoresis. The tryptic digests of the separated proteins were subjected to reflector matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis and the relative peak heights of cysteine-containing peptides were used to quantify their precursor proteins. This approach was tested for the relative quantification of proteins within an artificial mixture of standard proteins and for proteins observed in a 2-D map of rat serum. A good correlation was found between the measured ratios derived from MALDI-TOF data and those theoretically calculated prior to 2-D analysis via known mixing ratios of the two alkylating reagents. The described procedure has proved to be effective for comparative measurements of protein abundances within the investigated mixtures.     

Effect of ethanol on micellization and on decarboxylation of 6-nitrobenzisoxazole-3-carboxylate in aqueous cationic micelles

The effects of ethanol on the critical micellar concentration (cmc) and the rates of decarboxylation of 6-nitrobenzisoxazole-3-carboxylate (6-NBIC) have been investigated in aqueous cationic surfactants of the cetyltrialkylammonium family with bromide [CT(R)ABr], chloride [CT(R)ACl], and nitrate [CT(R)ANO3] counterions, and methyl (CTAX), n-propyl (CTPAX), and n-butyl (CTBAX) as the head group alkyl moieties. Effects upon cmc and reactivity are similar, featuring a break at the ethanol mole fraction, x(EtOH), of ca. 0.055; these effects have been related to changes in solvent structure, with formation of a clathrate at x(EtOH) = 0.055. Rate data in CTBABr were further investigated and fitting of raw kinetic data to the pseudophase model is possible up to x(EtOH) = 0.1, showing an unexpected decrease of rate constant values in the micellar pseudophase, kM', as ethanol content increases: a significant variation of micellar ionization degree could account for this kinetic effect.     

Matter-wave interferometer for large molecules

We demonstrate a near-field Talbot-Lau interferometer for C70 fullerene molecules. Such interferometers are particularly suitable for larger masses. Using three free-standing gold gratings of 1 microm period and a transversally incoherent but velocity-selected molecular beam, we achieve an interference fringe visibility of 40% with high count rate. Both the high visibility and its velocity dependence are in good agreement with a quantum simulation that takes into account the van der Waals interaction of the molecules with the gratings and are in striking contrast to a classical moiré model.     

Ab Initio calculations of the anisotropic dielectric tensor of GaAs/AlAs superlattices

The static dielectric properties of (001)(GaAs)(p)/(AlAs)(p) superlattices have been calculated as a function of their period p for 1< or = p < or =12, starting from density-functional theory. The interplay between quantum confinement and local field effects is shown to be crucial. For light polarized in the growth direction it leads to the otherwise surprising justification of the use of a classical effective medium theory, even for the smallest periods. Only the inclusion of both contributions allows in ab initio and in semiempirical calculations to reproduce the experimentally observed birefringence.     

Nuclear shielding and magnetic hyperfine structure of hydrogen cyanide

A millimeter-wave molecular beam maser has been used to resolve the magnetic hyperfine structure of hydrogen cyanide. The spin-rotation interaction constants have been measured for the three nuclei ¹⁴N, ¹³C, and H. The paramagnetic nuclear shielding factors have been calculated for the three nuclear sites. The spin-rotation constants for ¹⁴N in H¹²C¹⁴N, for H in H¹²C¹⁴N and for ¹³C in D¹³C¹⁴N are + 10.4 kHz, −3.7 kHz, and +15.0 kHz, respectively. The respective paramagnetic shielding factors are −408.98 × 10⁻⁶, −73.40 × 10⁻⁶, and −249.52 × 10⁻⁶.     

Backbone-only restraints for fast determination of the protein fold: the role of paramagnetism-based restraints. Cytochrome b562 as an example

CH(alpha) residual dipolar couplings (Deltardc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH(alpha) Deltardc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Deltardc's, which are largely isooriented within alpha helices. The whole structure is now significantly refined with the chemical shift index and CH(alpha) Deltardc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Deltardc's.     

The simulation of infrared bands from the analyses of rotational spectra: the 2ν9-ν9 and ν5-ν9 hot bands of HNO3

The results of millimeter and submillimeter wave rotational spectroscopy are used to simulate the complex structure of the 2ν₉-ν₉ and ν₅-ν₉ hot bands. The comparison data were obtained with a high-resolution Bruker FTIR. The combination of the quality of these data and the complexity of the spectra of these interacting states represents a stringent test for the simulation. It is shown that the agreement is very good and that this approach is generally advantageous. From this simulation, the ratios of the transition dipole moments for the 2ν₉-ν₉ and ν₅-ν₉ hot bands with respect to the ν₉ fundamental band were found to be 1.38(11) and 0.67(20), respectively. Using these results, the calculated integrated band intensities for the hot bands at were determined to be and . These results were used to successfully simulate high-resolution stratospheric spectra obtained from a balloon flight of the FIRS-2 spectrometer. The more general problem of the rotation-vibration database and the optimal use of both microwave and infrared data to define it is discussed. It is concluded that it is best if the combination of data takes place at the level of the original spectra.     

Synthesis of a first thiophene containing analog of the HIV protease inhibitor nelfinavir

A stereoselective and efficient preparation of a thiophene containing intermediate 2 from ethyl 3-thienyl propenoate 4 as the core of new possible HIV protease inhibitors is described. The chiral intermediate has been successfully used for the preparation of the analog 1 of the potent HIV inhibitor nelfinavir.     

From arm-shaped layers to a new type of polythreaded array: a two fold interpenetrated three-dimensional network with a rutile topology

The self-assembly based on 2D motifs with side arms leads to the formation of a new type of polythreaded network which exhibits a 2-fold interpenetrated 3D array if H-bonds are taken into account.