Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.      

Swelling Ratios and Rates of Sulfonation of Solvent Modified Copolymers of Styrene Cross-Linked with Pure m-and Pure p-Divinylbenzene

Solvent-modified (toluene) copolymers have been prepared from styrene cross-linked with commercial divinylbenzene, m-divinylbenzene, and p-divinylbenzene at divinyl monomer contents of 16 mole % and 32 mole % at F_M = 0.50. The resultant copolymers have been characterized by swelling-ratio determinations and rates of sulfonation at 60 and 80°C. The solvent-modified 16 mole % cross-linked copolymers sulfonated at rates slightly greater than those characterizing the 8 mole % cross-linked copolymers prepared in the absence of diluent. The order of decreasing sulfonation rates for both the conventional 8 mole % cross-linked systems and for the solvent-modified 16 mole % cross-linked copolymers is commercial divinylbenzene/styrene, p-divinylbenzene/styrene, m-divinylbenzene styrene. The 32 mole % cross-linked systems exhibit a different order of decreasing sulfonation rates: commercial divinylbenzene/styrene, m-divinylbenzene/styrene, p-divinylbenzene/styrene. The swelling ratios of the 32 mole % solvent-modified copolymers were comparable to those of the conventional 8 mole % cross-linked systems.     

Comparison of retention behavior of oligolysine and oligoarginine in ion-pairing chromatography using heptafluorobutyric acid

This paper describes the retention behavior of oligolysine and oligoarginine peptides of different lengths as a function of heptafluorobutyric acid (HFBA) concentration in ion-pairing reversed-phase chromatography in isocratic elution. A mixture of oligolysine and a mixture of oligoarginine with number of amino acid residues (dp) from two to eight were conveniently prepared by one-pot protease-catalyzed synthesis. Analysis of the logarithm of the retention factor k as a function of [HFBA] for each oligopeptide component, using a closed pairing model, provided values for (1) number (n) of paired HFBA anions per peptide molecule, (2) equilibrium constant (K _ip,m) for ion pairing between oligopeptides and HFBA anions, and (3) product of the phase ratio and the distribution constant of the paired oligopeptide between the mobile and stationary phases (βK _d,ip). We found that βK _d,ip of oligoarginine is larger compared with oligolysine having the same dp. A linear relationship was obtained for ln βK _d,ip as a function of n?+?g?·?dp. By optimizing constant g separately for oligolysine and oligoarginine, we determined that g is larger for oligoarginine, in agreement with the higher hydrophobicity of arginine residues. Plotting the fraction of paired oligoarginine and oligolysine as a function of [HFBA] shows that the cooperative effect in forming ion pairs is greater for oligoarginine than oligolysine.

PCR-based detection of gene transfer vectors: application to gene doping surveillance

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.     

Rapid phytochemical analysis of birch (Betula) and poplar (Populus) foliage by near-infrared reflectance spectroscopy

Poplar (Populus) and birch (Betula) species are widely distributed throughout the northern hemisphere, where they are foundation species in forest ecosystems and serve as important sources of pulpwood. The ecology of these species is strongly linked to their foliar chemistry, creating demand for a rapid, inexpensive method to analyze phytochemistry. Our study demonstrates the feasibility of using near-infrared reflectance spectroscopy (NIRS) as an inexpensive, high-throughput tool for determining primary (e.g., nitrogen, sugars, starch) and secondary (e.g., tannins, phenolic glycosides) foliar chemistry of Populus and Betula species, and identifies conditions necessary for obtaining reliable quantitative data. We developed calibrations with high predictive power (residual predictive deviations?≤?7.4) by relating phytochemical concentrations determined with classical analytical methods (e.g., spectrophotometric assays, liquid chromatography) to NIR spectra, using modified partial least squares regression. We determine that NIRS, although less sensitive and precise than classical methods for some compounds, provides useful predictions in a much faster, less expensive manner than do classical methods.

Progress in Parametric Pumping

Parametric pumping is the name given to a novel separation device developed by Richard Wilhelm and co-workers^(1,2,3). The principle of operation depends on an immobile phase (e.g. adsorbent) to alternately retard and release selected species. This action coupled with a synchronous periodic fluid flow causes the selectively adsorbed species to be literally pumped from one region to another. In the successful experiments^(2,3) a single packed column was used with reservoirs attached to each end. A water jacket surrounding the bed was heated or cooled synchronously with periodic fluid motion. Figure 1 outlines the principle of operation. Essentially, the process operates in a “bucket-brigade” fashion. If one follows the travels of a single solute (see Figure 1) in a non-adsorbable solvent we see that during downflow the column is cooled thus retarding (adsorption step) the solute, allowing the solvent to move unimpeded. When the flow direction changes to an upward motion, the column is heated, releasing (desorption step) the solute and sweeping it upward. Repeating this cycle, one sees that the solute hops in bucket-brigade fashion toward the upper reservoir until it is eventually captured. Separation factors (i.e., ratio of rich to lean reservoir composition) as large as 10⁵:1 have been reported^(2,3). The fundamental driving force for separation is the adsorbed phase concentration difference at the two operating temperatures. This difference depends on the shape of the isotherms as shown in Figure 2, The method of operation thus outlined has been called the direct thermal-mode⁽³⁾. The principle of operation is not limited to a thermally induced retardation-release step, and in fact Thompson and Bass^(4,5) recently used electrode potential to induce retardation. Furthermore, in a short note Lee and Kirwan⁽⁶⁾ outlined results whereby a porous carbon electrode sustained markedly different adsorption levels of biosubstances (glucoamylase) with Increases in applied voltage. In one of his earlier papers⁽³⁾, Wilhelm suggests a variety of driving potentials may be used, including electrical, pressure, magnetic, and chemical (e.g., pH). Obviously, any potential which can be effectively tuned so as to induce a retard-re lease mechanism could be used in designing a parametric pump. The trick is to discover a retardation-release mechanism which is selective, that is, only the desired species is pumped, while other species remain stagnant or move in the opposite direction (e.g., abnormal isotherm). By way of introduction, it should be noted that the parametric pumping technique is not limited to closed (batch) systems, but can be operated in a continuous and semi-continuous mode. Recent work on such open systems will also be treated in another section.     

At-line bioprocess monitoring by immunoassay with rotationally controlled serial siphoning and integrated supercritical angle fluorescence optics

In this paper we report a centrifugal microfluidic “lab-on-a-disc” system for at-line monitoring of human immunoglobulin G (hIgG) in a typical bioprocess environment. The novelty of this device is the combination of a heterogeneous sandwich immunoassay on a serial siphon-enabled microfluidic disc with automated sequential reagent delivery and surface-confined supercritical angle fluorescence (SAF)-based detection. The device, which is compact, easy-to-use and inexpensive, enables rapid detection of hIgG from a bioprocess sample. This was achieved with, an injection moulded SAF lens that was functionalized with aminopropyltriethoxysilane (APTES) using plasma enhanced chemical vapour deposition (PECVD) for the immobilization of protein A, and a hybrid integration with a microfluidic disc substrate. Advanced flow control, including the time-sequenced release of on-board liquid reagents, was implemented by serial siphoning with ancillary capillary stops. The concentration of surfactant in each assay reagent was optimized to ensure proper functioning of the siphon-based flow control. The entire automated microfluidic assay process is completed in less than 30 min. The developed prototype system was used to accurately measure industrial bioprocess samples that contained 10 mg mL⁻¹ of hIgG.     

Synthesis of Symmetrical and Unsymmetrical Ureas Using Unsymmetrical Diaryl Carbonates

Appropriately substituted unsymmetrical diaryl carbonates react smoothly with primary amines to give the carbamates derived by nucleophilic displacement of the less electron rich aromatic substituent. Subsequent treatment of the carbamates with primary and secondary amines gives either symmetrical or unsymmetrical ureas in excellent yield and the overall process can be carried out as a “one pot” operation. Acetonitrile is the preferred solvent and addition of DBU facilitates the carbamate → urea transformation.     

Halogenation of 2-Hydroxynicotinic Acid

A convenient method to prepare 5-halo-2-hydroxy-nicotinic acid is described.     

Amidrazones 9. Convenient Syntheses of 1-Alkyl-1-Phenylhydrazines and α,β-Unsaturated Amidrazones Via Base-Promoted Reactions of 1,1-Disubstituted-3-Amino-4,5-Dihydro-1H-Pyrazolium Salts

A simple, efficient procedure for the conversion of phenylhydrazine to 1-alkyl-1-phenylhydrazines via base-promoted hydrolysis of 1-alkyl-3-amino-4,5-dihydro-1-phenyl-1H-pyrazolium iodides (2) is described. N¹, N¹-disubstituted hydrazones of trans-cinnamamide and acrylamide are obtained by Hofmann-type ring openings of 1,1 -disubstituted-3-amino-4,5-dihydro-5-phenyl (or 5-unsubstituted) -1H-pyrazolium halides (5, 7).