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.     

The first kinetic evidence for acid catalysis in a monocyclic rearrangement of heterocycles: conversion of the Z-phenylhydrazone of 5-amino-3-benzoyl-1,2,4-oxadiazole into N,5-diphenyl-2H-1,2,3-triazol-4-ylurea

The title reaction has been studied in dioxane/water in a large (0.1-14.9) pS+ range, evidencing, together with an uncatalyzed process at intermediate (3.5-8.0) pS+ values, the occurrence of a catalyzed pathway both in the acidic (pS+ 0.1-3.5) and in the basic region (pS+ 8.0-14.9): specific-acid catalysis and general-base catalysis, respectively, have been found to take place by means of kinetic investigations at different buffer concentrations. Mechanisms for the three pathways have been advanced on the grounds of structural features. In a comparison with previous data particular attention has been paid to the acid-catalyzed pathway, herein observed for the first time in an azole-to-azole interconversion. The mechanistic hypotheses seem well supported by ab initio calculations.     

ISOLATION AND CHARACTERIZATION OF THE PRESUMED PHOTORECEPTOR PROTEIN OF Blepharisma japonicum

Abstract— Photosensory responses in the ciliated protozoan Blepharisma japonicum are mediated by a hypericin-like chromophore, blepharismin, localized in granules distributed under the cell membrane. A blepharismin-binding protein, with an apparcnt molecular weight ranging between 35 and 38 kDa, has been isolated by means of column separations and preparative isoelectric focusing and characterized by means of gel electrophoresis, analytic isoelectric focusing as well as absorption and fluorescence spectroscopy.     

The formation of proton and alkali metal complexes with ligands of biological interest in aqueous solution. Thermodynamics of Li+, Na+ and K+-dicarboxylate complex formation

The formation and stability of Li⁺, Na⁺ and K⁺ complexes with oxalate, malonate, succinate, maleate, DL-malate and phthalate were studied potentiometrically at various ionic strengths. From the data thus obtained, as well as from several literature data on the protonation of the above-mentioned ligands in various ionic media and at various temperatures, the dependence of Na⁺ and K⁺ complex formation on temperature was determined. The dependence on ionic strength, both for the protonation and the complex formation, is also discussed.     

Studies on comblike polymers. X. Characterization of comblike polyesters by 13C NMR spectroscopy

The ¹³C NMR spectra of aromatic comblike polyesters obtained from 1,2-icosanediol and isomeric phthalic acids are reported and discussed. The analysis shows that the most informative spectral regions are those of the carbonyl and quaternary carbon resonances, whose peak multiplicities have been interpreted in terms of dyad and triad sequences. The results indicate that the extent of structural characterization possible for the polymers examined is dependent on the type of isomerism of the aromatic acid involved.     

Regioselective synthesis of trisubstituted 2,3-dihydrofurans from donor-acceptor cyclopropanes or from reaction of the Corey ylide with alpha-sulfenyl-, alpha-sulfinyl-, or alpha-sulfonylenones

[reactions: see text] Regioselective synthesis of 2,4,5- or 3,4,5-trisubstituted 2,3-dihydrofurans has been realized by using donor-acceptor cyclopropanes or by a Corey ylide reaction with alpha-sulfenyl-, alpha-sulfinyl-, or alpha-sulfonylenones. The method allowed a straightforward synthesis of the natural product calyxolane B.     

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.     

Three-dimensional image fusion by use of multiwavelength digital holography

We present three-dimensional (3D) image fusion by use of digital holography. We demonstrate experimentally that, through the image fusion technique with multiresolution wavelet decomposition, it is possible to increase the details and contrast of 3D reconstructed images obtained by multiwavelength digital holography. Although there is substantial activity in the fields of image fusion and holography, to the best of our knowledge, this is the first report of 3D image fusion by use of digital holography.     

A simple geometrical model for emulsifier free polymer colloid formation

In this paper we propose a simple model for the formation of monodisperse polymer colloids, which provides a convenient set of synthetic parameters for given bead diameters. We provide experimental data in support of this model.