Simultaneous analysis of phosphoproteins and total cellular proteins from PC12 cells

The evolution of tools for protein phosphorylation site analysis: from discovery to clinical application

The importance of the analysis of signaling pathways has been proven for many years by the elucidation of key signaling molecules. However, in most cases these pathways tend to represent a rather narrow view of the biological state under investigation. Clearly a more detailed understanding of the complexities of cross-talk between signaling pathways is required to further our knowledge of normal and disease processes. The tools that provide the framework for this increased understanding of biology, those that enable identification, characterization, and quantitation of sites of phosphorylation in proteins, have advanced over the past 25 years. This review will present a brief overview of the history of the tools used in phosphorylation analysis and the latest technologies that are being applied in this field, such as mass spectrometry (for broad-based discovery efforts) and flow cytometry (for translation to clinical applications).

A personal journey of discovery: developing technology and changing biology

This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.

The assay development of a molecular marker for transmissible spongiform encephalopathies

The transmissible spongiform encephalopathies are a group of neurodegenerative diseases which include Creutzfeldt-Jakob disease (CJD) in humans, scrapie in sheep, and bovine spongiform encephalopathy (BSE) in cattle. Two-dimensional electrophoresis of proteins was previously used to identify two marker proteins, 130/131, which are selectively present in the cerebrospinal fluid (CSF) of patients with CJD and not in patients with other dementias. The recent characterization of these proteins by amino acid sequencing has identified them as members of the 14-3-3 family of proteins. Polyclonal antibodies against 14-3-3 (all isoforms), 14-3-3 gamma, 14-3-3 beta, and 14-3-3 theta are immunoreactive with a 30 kDa marker band from CJD CSF. Silver staining of two-dimensional electrophoresis separated BSE CSF proteins does not identify a similar marker. However, 14-3-3 immunoreactivity is found in cattle CSF when these proteins are blotted to polyvinylidene difluoride but not when blotted to nitrocellulose.

Glucocorticoid receptor phosphorylation in v-mos-transformed cells

Nucleocytoplasmic shuttling of glucocorticoid receptors (GRs) is disrupted in v-mos-transformed cells leading to the redistribution of hormone-bound receptors from the nuclear to cytoplasmic compartments. We show here that GRs from v-mos-transformed cells are hyperphosphorylated on a specific peptide and maintain hormone-induced phosphorylations upon a prolonged hormone treatment that is associated with disruptions in its nucleocytoplasmic shuttling. Since similar effects on GR nucleocytoplasmic shuttling and phosphorylation were exerted upon treatment of nontransformed cells with the protein phosphatase inhibitor okadaic acid, we examined whether hyperphosphorylation of GRs in v-mos-transformed cells resulted from inhibition of receptor dephosphorylation. Protein phosphatase activity, measured using various substrates in vitro, was identical in cell-free extracts prepared from v-mos-transformed and nontransformed cells. Analysis of phosphate turnover in vivo from either the sum of all GR phosphorylation sites or from individual sites using pulse-chase analysis, did not reveal any significant difference between v-mos-transformed cells versus nontransformed cells. Thus, hyperphosphorylation of GR in v-mos-transformed cells does not appear to result from inhibition of GR dephosphorylation, but rather from stimulation of GR phosphorylation.

Staining methods in gel electrophoresis, including the use of multiple detection methods

Polyacrylamide gel electrophoresis is a reliable and widely used technique for the separation, identification and characterization of proteins and protein mixtures. With the introduction of high resolution two-dimensional polyacrylamide gel electrophoresis in 1975 upward to 2000 individual polypeptides spots are easily separated on a single electrophoretic gel thereby necessitating the availability of highly sensitive protein detection methods. Although a plethora of protein-staining and -visualization protocols have been described utilizing both radioactive and non-radioactive reagents, many times the use of mono-dimensional detection procedures is insufficient to address the experimental questions asked. The present review highlights the utilization of combined protein-labeling and -staining methodologies in gel electrophoresis including selected applications in polyacrylamide gels and solid membrane matrixes.

The sea urchin profilin gene is specifically expressed in mesenchyme cells during gastrulation

Eggs and embryos of the purple sea urchin (Strongylocentrotus purpuratus) contain profilin that is partly supplied from maternal sources and partly produced by the gastrula. The maternal profilin protein content is about 13 microM and it persists in the embryo at least through gastrulation. Transcript quantitation from probe excess titrations show that very few profilin gene transcripts are present in the embryo during cleavage, but that they increase at the onset of gastrulation. By in situ hybridization, the newly synthesized profilin transcripts are localized in mesenchyme cells. Profilin gene expression increases when mesenchyme cells initiate migration and filopodial extension and retraction. We show that there are three isoforms of maternal profilin protein produced from the single copy gene during oogenesis. However, the blastula stage embryo only produces the major isoform, whereas the acidic isoform is produced in the early stages of gastrulation and the basic isoform appears by the end of gastrulation. Based on transcript prevalence and protein production rates, our calculations indicate that the amount of new protein produced in the mesenchyme cells in 12 hr is at maximum < 2% of that supplied from maternal sources. Because of the large amount of maternally supplied profilin present in the egg and embryo, we suggest that it may be used in the cytokinetic processes of cleavage. Alternatively, because of the small amount of embryonically produced profilin, we suggest that it may function in the cytoskeletal shape changes required for filopodial extension and motility in the mesenchyme cells during gastrulation.