Analytical methods for differentiating minor sequence variations in related peptides

Biomolecular interaction analysis of IFN gamma-induced signaling events in whole-cell lysates: prevalence of latent STAT1 in high-molecular weight complexes

The basic framework for the JAK/STAT pathway is well documented. Recruitment of latent cytoplasmic STAT transcription factors to tyrosine phosphorylated docking sites on cytokine receptors and their JAK-mediated phosphorylation instigates their translocation to the nucleus and their ability to bind DNA. The biochemical processes underlying recruitment and activation of this pathway have commonly been studied in reconstituted in vitro systems using previously defined recombinant signaling components. We have dissected the Interferon gamma (IFN gamma) signal transduction pathway in crude extracts from wild-type and STAT1-negative mutant cell lines by real-time BIAcore analysis, size-exclusion (SE) chromatography and immuno-detection. The data indicate that in detergent-free cell extracts: (1) the phospho-tyrosine (Y440P)-containing peptide motif of the IFN gamma-receptor alpha-chain interacts directly with STAT1, or STAT1 complexes, and no other protein; (2) non-activated STAT1 is present in a higher molecular weight complex(es) and, at least for IFN gamma-primed cells, is available for recruitment to the activated IFN gamma-receptor from only a subset of such complexes; (3) activated STAT1 is released from the receptor as a monomer.

Reassessment of cytochrome P450 2B2: catalytic specificity and identification of four active site residues

Cytochromes P450 2B metabolize a variety of compounds and have provided an excellent framework for identifying determinants of substrate specificity. Among the rat 2B enzymes, a puzzling difference has emerged between the reported substrate specificity of purified hepatic 2B2 and that of certain 2B1 mutants containing 2B1 --> 2B2 substitutions. To address these discrepancies, we have characterized two 2B2 variants. A cDNA clone designated 2B2FF was obtained from phenobarbital-induced Lewis rats and, like some previously isolated variants, was found to contain phenylalanine at positions 58 and 114. A second 2B2 clone was generated by restoring Leu and Ile, respectively, at these positions. These enzymes were expressed in Escherichia coli and analyzed with androstenedione, testosterone, progesterone, ethoxycoumarin, benzyloxyresorufin, and pentoxyresorufin. The expressed 2B2 variants metabolized most substrates at rates that were 1-9% of those of 2B1. When steroid regio- and stereospecificity was examined, the metabolite profiles of expressed 2B2 and 2B2FF conflicted with the 16beta- and 16alpha-hydroxylation observed for purified hepatic 2B2 from Sprague-Dawley rats. These and other results suggested that the purified hepatic 2B2 contained a small percent of the 2B1 enzyme. Masses of tryptic peptides were consistent with identity between purified hepatic 2B2 and 2B2FF. On the basis of a three-dimensional homology model and the construction and analysis of 2B2 mutants, residues 114, 363, 367, and 478 were identified as determinants of substrate specificity. In addition, 2B1 and the expressed 2B2 variants showed differential susceptibility to the mechanism-based inactivators chloramphenicol and N-(2-p-nitrophenethyl)chlorofluoroacetamide.

Biomedical and biochemical applications of liquid chromatography-mass spectrometry

This review centres on the application of various LC-MS and LC-MS-MS techniques to the study and solution of practical problems in biomedical research. For this purpose it covers a selection of publications in this area included in the MEDLINE database for the period 1991-mid-1994. As shown herein, LC-MS is increasingly gaining in importance in the biomedical field, especially after the revolution brought about by the introduction of the new liquid-phase atmospheric pressure ionization (API) techniques, such as electrospray (ES) and ionspray. The information in this database shows that thermospray (TS), which clearly dominated LC-MS coupling in the 1980s, is on a downward trend relative to the more modern API techniques which will certainly dominate this application field in the present decade. Studies on drug metabolism, therapeutic drug monitoring and pharmacology have been traditionally carried out by GC-MS. However, LC-MS has lately been replacing classical GC-MS techniques in many of these applications. For instance, LC-ES-MS has greatly facilitated the application of both qualitative and quantitative LC-MS methods to highly polar molecules. This is possible without the need to resort to elaborate sample handling and derivatization procedures for relatively high-molecular-mass compounds such as drug conjugates, biosynthetic and natural peptides and therapeutic proteins obtained by recombinant DNA technology, all of them formerly totally inaccessible to the standard GC-MS or LC-MS methods. With regard to studies on metabolism and biochemical phenomena of endogenous compounds, LC-ES-MS is also becoming very strong in the analysis of structural biopolymers such as peptides, proteins, glycoproteins and glycolipids, and also lower molecular mass compounds such as fatty acids, vitamins, steroids and nucleic acids. For example, structural verification of post-translational modifications in proteins can be efficiently obtained in the time frame of an LC run and suitable MS methods for the location of glycopeptide-containing fractions in proteolytic digests of glycoproteins have been developed. Interesting examples are also shown of the use of LC-MS in clinical studies and the determination of biological markers of disease.