iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing

Immobilized pH gradient isoelectric focusing (IPG-IEF) has emerged as a highly promising alternative to strong-cation exchange fractionation as the first dimension in shot-gun proteomics. Herein is shown the compatibility of this method with iTRAQ isotope labeling for relative quantitation and validation of sequence matches from database searching.     

Spirocamallanus cricotus (Nematoda): isoelectric focusing and spectrophotometric characterization of its hemoglobin and that of its piscine host, Micropogonias undulatus

The hemoglobins of Spirocamallanus cricotus, a reddish-colored, camallanid nematode, and its Atlantic croacker fish host, Micropogonias undulatus, were characterized with spectrophotometry and isoelectric focusing. Hemoglobin from female parasites' perienteric fluid and homogenized male parasites gave Spectrophotometric peaks at 412, 539, and 575 nm, whereas female worms drained of perienteric fluid and homogenized differed by having a Soret peak of 408 nm. Changing the ionic strength of the buffer from 0.1 to 0.01 M shifted the Soret peak to 406 nm for the female parasites' perienteric fluid and ground male parasites and 404 nm for homogenized female parasites. In all cases, the β band had a higher absorption than the α band suggesting a high O₂ affinity for the parasite hemoglobin. Host hemoglobin had peaks of 406, 437, and 577 nm. Isoelectric focusing not only confirmed the Spectrophotometric evidence that host and parasite hemoglobins differed, but also showed that the parasite's analyzed hemoglobin fractions differed from one another by having different isoelectric points.     

Comparison of <Emphasis Type="Italic">Escherichia coli,Saccharomyces cerevisiae,Pichia pastoris,Spodoptera frugiperda</Emphasis>, and COS7 cells for recombinant gene expression

Expression of a rabbit liver carboxylesterase has been achieved in several different model systems including Escherichia coli, Pichia pastoris, Saccharomyces cerevisiae, Spodoptera frugiperda, and COS7 cells. Although, recombinant protein was observed in E. coli sonicates, little or no enzymatic activity was detected. Similarly, no activity was observed following expression in S. cerevisiae. In contrast, active protein was produced in P. pastoris from S. frugiperda, following baculoviral infection and in COS7 cells following transient transfection of plasmid DNA. For the preparation of small amounts of protein for kinetic and biochemical studies, enzyme expressed in P. pastoris has proved sufficient. However, to produce large amounts of carboxylesterase for structural studies, baculoviral-mediated expression of a secreted form of the protein in S. frugiperda was the most efficient. Using this system, we have generated and purified milligram quantities of essentially pure protein. These results demonstrate that the choice of in vitro system for the generation of large amounts of active carboxylesterase, and probably most endoplasmic reticulum processed proteins, is crucial for high level expression and subsequent purification.     

A three-step purification of human alpha 1-acid glycoprotein

alpha 1-Acid glycoprotein (AGP) was purified to homogeneity by a 3-step procedure using pseudo-ligand affinity chromatography on immobilized Cibacron blue F3GA, Procion red HE3B, and preparative column isoelectric focusing. The overall yield of the combined techniques was 88%. Analysis of the purified AGP by lectin affinity chromatography on immobilized Con A and immunoaffino-electrophoresis indicated that the most acidic form did not interact with the lectin, while the two more basic fractions possessed different affinities for Con A. In addition, 3 different populations of AGP were clearly separated by Con A affinity chromatography.     

Genetic relationships among species of hagfish revealed by protein electrophoresis

Hagfish species of the genera Myxine, Eptatretus and Paramyxine were analysed for genetic variation by allozyme electrophoresis and isoelectric focusing of general proteins. Large genetic differences were observed between samples of supposed conspecifics of Myxine circifrons from off the Californian coast, and also within one sample of Paramyxine sp. from Sagami Bay, Japan. The results are convincing evidence of the existence of additional sympatric species in these two areas. In general, the highest genetic identities were found between species within the subfamilies Myxininae and Eptatretinae. Within Eptatretinae, the Japanese species Eptatretus burgeri was genetically more similar to Japanese species of Paramyxine than to American species of Eptatretus . Thus, our data indicate that the generic status of Paramyxine should be reconsidered.     

A mutation affecting the lactate dehydrogenase locus Ldh-1 in the mouse—I. Genetical and electrophoretical characterization

(101/El × C3H/El)F₁ male mice were injected intraperitoneally with the mutagen procarbazine hydrochloride and immediately caged with untreated test-stock females. Crude liver extracts from the offspring were subjected to polyacrylamide gel isoelectric focusing, and the gels were stained for six enzymes. In the experimental group (mutagen treated spermatogonial germ-cell stage), a dominant inherited banding alteration of the lactate dehydrogenase (LDH) pattern was detected. By crossing the heterozygous mutants, homozygotes were obtained that showed much less gel staining intensity. The mutation is codominantly expressed with 100% penetrance. The banding alteration was also observed in muscle, kidney, heart, blood, brain, testis, spleen, and lung. Polyacrylamide gel electrophoresis was performed with all the tissues examined. The mutation causes the intensity of the band corresponding to LDH-A (primary molecular form in muscle) to decrease from that of the wild type, while the intensity of the bands corresponding to LDH-B (primary molecular form in heart) remains constant. It is concluded that the mutation affects the locus coding for LDH of the muscle type. Ldh-1 ^c is proposed as the allele symbol.     

Two-dimensional maps in very acidic immobilized pH gradients

Up to the present time it has been impossible to perform two-dimensional (2-D) separations in very acidic immobilized pH gradients (IPG), due to the lack of suitable buffering acrylamido derivatives to be incorporated into the polyacrylamide matrix. The advent of the pK 3.1 buffer (2-acrylamido glycolic acid; Righetti et al., J. Biochem. Biophys. Methods 16, 1988, 185–192) allowed the formulation of such acidic gradients. We report here separations in IPG pH 2.8–5.0 intervals of polypeptide chains from total lysates of rat intestinal and liver cells and 30S and 50S ribosomal proteins from Halobacterium marismortui. Conditions are given for highly reproducible first and second dimensions gels and for a proper silver staining of 2-D maps with practically no background deposition.     

Brain Tubulin Microheterogeneity in the Mouse During Development and Aging

Abstract: Mouse brain tubulin was analyzed on isoelectric focusing gels. High-resolution gels utilizing Bio-Rad ampholytes (pH 4-6) revealed 5-6 bands in the region corresponding to the α-subunit of tubulin and 10 or more for the β-subunit. The same general banding pattern was observed regardless of the method of preparation of the tubulin. Two species prominent in the brains of immature mice, α6 and β2, virtually disappeared during maturation, while species β6 to β10 appeared. No significant changes from the mature pattern were seen during aging (examined at 12, 23, and 30 months of age).     

Functional properties of the newly observed γ-chain fetal hemoglobin variant Hb F-Monserrato-Sassari (HBG2:c.280T > C) or [γ93 (F9) Cys → Arg]

Background

HbF-Monserrato-Sassari is a newly discovered abnormal fetal hemoglobin observed in an apparently normal newborn baby during a hemoglobinopathies survey at birth in North Sardinian population.

Methods

Electrophoretic analysis of the cord blood lysate evidenced for an abnormal tetramer due to a mutated fetal globin chain. Electrospray ionisation-mass spectrometry and gene sequencing were used to identify the mutation. Oxygen binding ability of the variant Hb was determined.

Results

Sequencing of the γ globin genes revealed the TGT → CGT transition at codon 93 in one of the two ^Gγ genes, which leads to the Arg for Cys amino acid replacement at position 9 of the F α-helix. The amino acid substitution was confirmed by mass spectrometric analysis of the globin chains. Since modifications or substitutions at position β93 are known to affect the arrangement of a salt bridge at the α1β2 sliding contacts that are crucial for subunit cooperativity, the functional properties of the variant were studied to evaluate the effect of the replacement at the same position in the γ globin chain. With respect to normal HbF, the variant showed a significant increase in oxygen affinity and a slight decrease of both Bohr effect and cooperativity.

General significance

Result indicates a key role of the Cys γ93 residue for subunit cooperativity in the T → R transition of the HbF tetramer. Substitutions at the F9 position of the ^Gγ globin may result in stabilization of the high affinity R-state of the Hb tetramer. Because of the loss of Cys γ93 residue, this variant is considered to be potentially compromised in nitric oxide transport.     

Optimized isolation procedure for obtaining strongly actinide binding exopolymeric substances (EPS) from two bacteria (Sagittula stellata and Pseudomonas fluorescens Biovar II)

Different chemical extractants (NaCl, EDTA, HCl and NaOH) and physical methods (ultrasonication and heating) were examined by their efficacies of extracting “attached” exopolymeric substances (EPS) secreted by marine bacterium Sagittula stellata (SS) and terrestrial bacterium Pseudomonas fluorescens Biovar II (PF). Extraction by 0.5 N HCl for 3 h was best for SS while extraction by 0.05 N NaCl for 3–5 h was regarded as optimal for PF. Improvements in EPS purification included a pre-diafiltration step to remove the broth material and reduce the solution volume, thus the usage of ethanol, and time. The EPS harvested at the optimal time and purified by the improved method were enriched in polysaccharides, with smaller amounts of proteins, thus having amphiphilic properties. Isoelectric focusing of ²³⁴Th or ²⁴⁰Pu labeled EPS showed both actinides were strongly bound to macromolecules with low pI, similar to reported marine or soil colloidal natural organic matter (NOM).