A simple, inexpensive method for the salt-free concentration of proteins for analysis by two-dimensional gel electrophoresis

Picking vanished proteins from the void: how to collect and ship/share extremely dilute proteins in a reproducible and highly efficient manner

Successful proteome analyses of highly dilute samples are strongly dependent on optimized workflows considering especially sample preparation prior to highly sensitive mass spectrometric analysis. Various methods are available for enrichment of proteome samples, each characterized by specific advantages and disadvantages limiting their general application as a method of choice. Here we suggest an optimized universal protocol ensuring reproducibility and effective enrichment of dilute samples by commercial affinity beads. By comparably assessing the performance of the new protocol with selected standard enrichment techniques, we show the seamless application of the enrichment in common mass spectrometry based proteomic workflows. Further, novel applications are suggested including a facile storage and shipping of desiccated, trapped proteome samples at ambient temperatures and usage of the affinity beads for gel-free proteomic approaches.

Electrical conductivity as a tool to detect salt in clinical proteomics samples

Clinical proteomics encompasses the study of the proteins in the human body at different settings to understand the various physiological and pathological pathways. The processing of the samples for electrophoresis based proteomics is a challenge to any researcher. Salt in particular can have an array of effects during the electrophoretic separation of proteins. There is a definite need to determine the concentration of salts in the samples and the effectiveness of salt removing protocols on small volume samples. A simple-cost effective technique to know the salt concentration in the clinical proteomics samples has been highlighted in the report. The application will be of value in a developing country such as India.

Preparing protein extracts for quantitative two-dimensional gel comparison

This unit describes basic protocols for efficient and reproducible protein solubilization from a variety of biological samples, including cultured animal cells and tissues, plant cells and tissues, bacteria, nuclei, other subcellular organelles, plasma, serum, and other biological fluids. The optimized extraction process is strongly sample-dependent and cannot be described for every type of sample. Instead, typical protocols are provided as general guidelines and illustrate good starting points for sample-preparation optimization. These solubilization procedures take into account the constraints brought by two-dimensional electrophoresis and are thus well suited for proteomic approaches.

Toward a better analysis of secreted proteins: the example of the myeloid cells secretome

The analysis of secreted proteins represents a challenge for current proteomics techniques. Proteins are usually secreted at low concentrations in the culture media, which makes their recovery difficult. In addition, culture media are rich in salts and other compounds interfering with most proteomics techniques, which makes selective precipitation of proteins almost mandatory for a correct subsequent proteomics analysis. Last but not least, the non-secreted proteins liberated in the culture medium upon lysis of a few dead cells heavily contaminate the so-called secreted proteins preparations. Several techniques have been used in the past for concentration of proteins secreted in culture media. These techniques present several drawbacks, such as coprecipitation of salts or poor yields at low protein concentrations. Improved techniques based on carrier-assisted TCA precipitation are described and discussed in this report. These techniques have been used to analyze the secretome of myeloid cells (macrophages, dendritic cells) and enabled to analyze proteins secreted at concentrations close to 1 ng/mL, thereby allowing the detection of some of the cytokines (TNF, IL-12) secreted by the myeloid cells upon activation by bacterial products.

Altered patterns of proteins released in vitro from oviductal and uterine tissue from adult female mice treated neonatally with diethylstilbestrol

Proteins released during incubation in vitro of oviductal and uterine tissues from 8-week-old female NMRI mice treated neonatally with diethylstilbestrol (DES) or vehicle were studied. The objective was to study if neonatal DES treatment altered the patterns of proteins released from the oviduct and uterus, as earlier studies had shown a detrimental effect of the oviductal environment in DES exposed females on early embryo development. In separate experiments nonlabeled and 35S-labeled proteins released from oviductal/uterine tissues during organ incubations were characterized with 1 and 2D gel electrophoresis. The incubation media of both oviducts and uteri from DES females had increased levels of a serum derived nonlabeled protein, identified as apolipoprotein A1. The amount of this protein in the incubation medium was not influenced by previous ovariectomy but increased by in vivo treatment with estradiol, in both ovariectomized controls and DES treated females. Three other unlabeled proteins were consistently found in higher amounts in the incubation media from DES exposed oviduct/uterine tissue, than in incubates of control tissue. In tissue incubates of oviducts from DES females, three synthesized proteins (35 kDa-pl 6.2, 112 and 143 kDa) were released in lower amounts and two in higher amounts (53 kDa-pl 6.6 and 53 kDa-pl 6.8) than in controls. In uterus from DES treated females one labeled protein was released in increased amounts (80 kDa-pl 6.7) and one in decreased amounts (43 kDa-pl 6.6), when compared with controls. In estrogen induced uterine luminal fluid from 8-week-old DES treated females the levels of four proteins (26, 42, 53 and 97 kDa) were increased and two (24 and 32 kDa) were decreased. These results show permanent alterations in levels of secreted proteins in both the oviduct and uterus of adult but neonatally DES treated females, which could be of importance for their poor reproductive performance.

Two-dimensional electrophoresis as a tool for control of quality and consistency in production systems using animal cells

A nonrecombinant human melanoma cell line and recombinant chinese hamster ovary (CHO) cells were used as examples for long-term in vitro cultivation in protein-free media. The method used to monitor the consistency of protein release by these mammalian cells was two-dimensional electrophoresis with immobilized pH gradient. Secreted proteins from a melanoma cell line cultivated in a continuous fermentation system over a period of 22 months were monitored. Two-dimensional patterns of secreted proteins were compared and the stability of their composition was determined over a period of nearly 14 months, with significant pattern variation being observed after 14 months. The protein pattern from this extended in vitro culture was compared to those of the very same melanoma cell line recultivated after being frozen in liquid nitrogen for more than 2 years. Due to the high resolution of complex polypeptide mixtures and the possibility to detect even minor differences in the composition of protein patterns, we propose the two-dimensional electrophoresis as a tool for quality assessment in animal cell culture technology.

Comparative biochemical and immunological studies on gamma-glutamyltransferases from human kidney and renal cell carcinoma applying monoclonal antibodies

We have purified gamma-glutamyltransferases (GGT) from human kidneys and renal cell carcinomas, and fractionated them according to different lectin-binding properties of the isoenzymes. Native polyacrylamide gel electrophoresis and isoelectric focusing revealed different GGT-bands (even after desialylation) not only among kidney and renal carcinoma, but also among Con A-affine tumor fractions separated by ion-exchange chromatography. Mr of native GGTs were between 106 to 161 kDa, the pI ranged from pH 3 to 4 (pH 5 to 6 after desialylation). Monoclonal antibodies to GGT were produced. One of these, of IgG1 class and designed 138H11, recognizes human kidney GGT and, in addition, GGT from renal cell carcinomas and liver carcinomas. The specificity of mAb 138H11 for GGT was confirmed by Western blotting, by immunohistochemistry and by immunoprecipitation. The potential usefulness of mAb 138H11 in monitoring renal cancer patients and in identification of renal cancer metastases is currently being studied.

Altered synthesis of the 26-kDa heat stress protein family and thermotolerance in cell lines with elevated levels of calcium-binding proteins

Using a bovine papilloma virus-based vector, mouse mammary adenocarcinoma cells have been transformed to express elevated amounts of functional calmodulin (CaM) (Rasmussen and Means, 1987) and another Ca2(+)-binding protein, parvalbumin (PV) (Rasmussen and Means, 1989) that is not normally synthesized in these cells. Parental cells (C127) and cells transformed by the vector alone (BPV-1), the vector containing a CaM gene (CM-1), or the vector containing parvalbumin (PV-1) were used to study the effect of increased synthesis of Ca2(+)-binding proteins on heat-stress protein (HSP) synthesis and cell survival following heating at 43 degrees C. The induction, stability, and repression of the synthesis of most HSPs after 43 degrees C heating was not significantly affected by increased amounts of Ca2(+)-binding proteins, but the rate of synthesis of all three isoforms of the 26-kDa HSP (HSP26) was greatly reduced. C127 cells, which have about one half as much CaM as do BPV-1 cells, synthesized the most HSP26. CM-1 cells, which have more than fourfold higher levels of CaM than do BPV-1 cells, had a rate of synthesis of HSP26 approaching that of unheated cells. BPV-1 cells, with a two-fold increase in CaM, were intermediate in HSP26 synthesis. This effect on HSP26 synthesis may be largely related to the Ca2(+)-binding capacity of CaM rather than to a specific CaM-regulated function, since PV-1 cells also showed reduced rates of HSP26 synthesis. Survival experiments showed that reduced HSP26 synthesis in cells with increased amounts of Ca2(+)-binding proteins did not significantly alter intrinsic resistance to continuous 43 degrees C heating. Thermotolerance was not reduced and appeared to develop more rapidly in CM-1 and PV-1 cells. These results suggest that (1) the signal for HSP26 synthesis can be largely abrogated by elevated Ca2+ binding protein levels, and (2) if these HSPs are involved in thermotolerance development, that function may be associated with intracellular Ca2+ homeostasis.

The effect of calmodulin antagonists on hyperthermic cell killing and the development of thermotolerance

The role of calmodulin (CaM) in hyperthermic cell killing, and the development of thermotolerance in rat 13762NF mammary adenocarcinoma cells, was investigated by using the CaM antagonists W-7 [N-(6-aminohexyl)-5-chloro-1-naphthalene sulphonamide] and W-13 [N-(4-aminobutyl)-2-chloro-naphthalenesulphonamide] and their less active analogues W-5 [N-(6-aminohexyl)-1-naphthalenesulphonamide] and W-12 [N-(4-aminobutyl)-2-naphthalenesulphonamide]. The CaM antagonists W-7 and W-13 potentiated 43 degrees C cell killing (and the less active analogues did not) at a concentration compatible with CaM inhibition, thus hyperthermic perturbation of CaM-regulated processes may contribute to cellular lethality. The potentiation of hyperthermic killing by antagonists appeared to be temperature-dependent, sensitizing much more effectively to 43 degrees C than to 42 degrees C killing. The effect may be related to differing primary mechanisms of hyperthermic killing activated at the two temperatures, or simply to differences in incorporation or localization of the antagonists. The presence of the CaM antagonists throughout fractionated 42 degrees C or 43 degrees C heating, or during continuous 42 degrees C heating, did not significantly inhibit or potentiate the triggering and development of thermotolerance or alter the rates of heat stress protein (HSP) synthesis. Studies using CaM-agarose isolation of CaM-binding proteins indicated that binding of some HSP to CaM-agarose occurred and was Ca2+-dependent. The specificity and physiological relevance of these HSP binding to CaM was not clear, since their affinity was not high in these cells. Presumably W-7 would perturb any physiologically relevant CaM-protein interactions in cells but W-7 concentrations that reduced HSP and other protein binding to CaM-agarose columns by 50 per cent or more, had no effect on thermotolerance development in cells. These observations, combined with the studies that showed little effect of CaM antagonists on HSP synthesis at concentrations which potentiated cell killing, suggested that events leading to triggering or developing thermotolerance were not strongly dependent on any putative HSP binding to CaM. These studies also suggest some targets of hyperthermic cell killing at 43 degrees C are different from those that lead to the triggering and development of thermotolerance.

Cerebrospinal fluid protein analysis in diseases of the nervous system

Electrophoretic studies of human CSF proteins from patients with diseases of the NS are reviewed. Various 1-DE methods are of similar value in identifying the non-specific OBs, which are helpful in the diagnosis of MS and recurrent GBS. In early and subclinical MS, OBs are of prognostic value, with IEF gels having the greater resolution. Silver-stained 2-DE gels provide the equivalent information to the OBs on 1-DE gels, with even greater sensitivity, and yield additional disease-associated protein data. Two proteins have proven to have diagnostic value in CJD and other changes that are still being evaluated have been identified in Parkinson's disease, GBS, Alzheimer's disease, schizophrenia and Herpes simplex encephalitis. The vastly improved CSF protein information obtained with silver-stained 2-DE gels heralds both a change from the relatively limited applications with 1-DE methods and also the need to adopt this approach in the routine clinical laboratory.