Antibodies directed against phosphothreonine residues as potent tools for studying protein phosphorylation

Empirical Evidence of Cellular Histidine Phosphorylation by Immunoblotting Using pHis mAbs

Immunoblotting is a ubiquitous immunological technique that aids in detecting and quantifying proteins (including those of lower abundance) and their posttranslational modifications such as phosphorylation, acetylation, ubiquitylation, and sumoylation. The technique involves electrophoretically separating proteins on an SDS-PAGE gel, transferring them onto a PVDF (or nitrocellulose) membrane and probing with specific antibodies. Here we describe an immunoblotting technique for detecting cellular phosphohistidine, a labile posttranslational modification, by optimizing experimental conditions such that the labile phosphohistidine signal is conserved throughout the experiment.

A systematic understanding of signaling by ErbB2 in cancer using phosphoproteomics

ErbB2 is an important receptor tyrosine kinase and a member of the ErbB family. Although it does not have a specific ligand, it transmits signals downstream by heterodimerization with other receptors in the family. It plays a major role in a variety of cellular responses like proliferation, differentiation, and adhesion. ErbB2 is amplified at the DNA level in breast cancer (20%–30%) and gastric cancer (10%–20%), and trastuzumab is effective as a therapeutic antibody. This review is a critical analysis of the currently published data on the signaling pathways of ErbB2 and the interacting proteins. It also focuses on the techniques that are currently available to evaluate the entire phosphoproteome following activation of ErbB2. Identification of new and relevant phosphoproteins can not only serve as new therapeutic targets but also as a surrogate marker in patients to assess the activity of compounds that inhibit ErbB2. Overall, such analysis will improve understanding of signaling by ErbB2.

Peptoid ligands that bind selectively to phosphoproteins

Synthetic equivalents of phosphoprotein-specific antibodies would be valuable reagents for biological research, since these antibodies can often be difficult to produce. Protein phosphorylation is thought to result in significant conformational changes in most substrate proteins. Therefore, one approach might be to simply screen combinatorial libraries for ligands to the phosphorylated state in the hope of isolating a ligand that binds to a pocket created by the conformational shift. In this study, we probe this strategy by screening a peptoid library for ligands to the phosphorylated form of the Brd4 chromatin adaptor and transcriptional coactivator protein. We find that peptoids with high selectivity for binding to the phosphorylation form of Brd4 can indeed be isolated in this screen. Moreover, these ligands do not bind promiscuously to other phospho-proteins. However, attempts to employ these reagents as antibody substitutes in an immunoaffinity purification-like application showed that they do not perform as well as bona fide antibodies and that significant optimization will be required. This study highlights the potential and current limitations of a naïve library screening strategy for phosphoprotein-specific antibody surrogates.

Reporting from the field: genetically encoded fluorescent reporters uncover signaling dynamics in living biological systems

Real-time visualization of a wide range of biochemical processes in living systems is being made possible through the development and application of genetically encoded fluorescent reporters. These versatile biosensors have proven themselves tailor-made to the study of signal transduction, and in this review, we discuss some of the unique insights that they continue to provide regarding the spatial organization and dynamic regulation of intracellular signaling networks. In addition, we explore the more recent push to expand the scope of biological phenomena that can be monitored using these reporters, while also considering the potential to integrate this highly adaptable technology with a number of emerging techniques that may significantly broaden our view of how networks of biochemical processes shape larger biological phenomena.

Phosphoproteomics, oncogenic signaling and cancer research

The past 5 years have seen an explosion of phosphoproteomics methods development. In this review, using epidermal growth-factor signaling as a model, we will discuss how phosphoproteomics, along with bioinformatics and computational modeling, have impacted key aspects of oncogenic signaling such as in the temporal fine mapping of phosphorylation events, and the identification of novel tyrosine kinase substrates and phosphorylation sites. We submit that the next decade will see considerable exploitation of phosphoproteomics in cancer research. Such a phenomenon is already happening as exemplified by its use in promoting the understanding of the molecular etiology of cancer and target-directed therapeutics.

Immunological detection of phosphorylation

Incorporation of phosphates into serine, threonine, and tyrosine acceptors in proteins is a common mechanism for regulating protein function. This unit presents protocols that use specific anti-phosphoamino acid (PAA) and anti-phosphoprotein antibodies to detect protein phosphorylation and protein kinase activity. Immunoblotting to detect protein phosphorylation using either anti-PAA or anti-phosphoprotein antibodies. This is a convenient method that usually yields impressive results. Phosphorylation can also be detected by immunoprecipitation followed by immunoblot analysis or by immunofluorescent staining; these methods are typically more complicated and time consuming. All three methods have been successfully used to detect protein phosphorylation with a wide variety of antibodies and most phosphorylated proteins.

Current methods for phosphoprotein isolation and enrichment

The phosphorylation of proteins is a central paradigm of signal transduction. The substitution of neutral hydroxyl groups of serine, threonine and tyrosine with a negatively charged phosphate group alters the physicochemical and immunogenic properties of the protein, which then can be used to isolate these isoforms. In the last decades several different techniques were applied, attempting to selectively enrich protein populations with this post-translational modification. This review aims to give an overview on the arsenal of available methods to extract phosphoproteins focusing on chromatographic approaches.

Phosphorylation state-specific antibodies: applications in investigative and diagnostic pathology

Until recently, the investigation of protein phosphorylation was limited to biochemical studies of enzyme activities in homogenized tissues. The availability of hundreds of phosphorylation state-specific antibodies (PSSAs) now makes possible the study of protein phosphorylation in situ, and is opening many exciting opportunities in investigative and diagnostic pathology. This review illustrates the power of PSSAs, especially in immunohistochemical applications to human disease and animal models. Technical considerations, including antibody specificity and lability of phosphoepitopes, are covered, along with potential pitfalls, illustrated by a case study. In the arena of oncology, PSSAs may prove especially valuable in directly demonstrating the efficacy of chemotherapies targeted at protein kinase cascades. Novel applications of PSSAs are also beginning to reveal molecular mechanisms of inflammatory, degenerative, and toxin-induced diseases.

Site-specific anti-phosphopeptide antibodies: use in assessing insulin receptor serine/threonine phosphorylation state and identification of serine-1327 as a novel site of phorbol ester-induced phosphorylation

Rabbit antisera were raised against synthetic phosphopeptides corresponding to defined or putative sites of insulin receptor serine/threonine phosphorylation (Ser-1305, Ser-1327, Thr-1348). All of these antibodies bound specifically to the immunogenic phosphopeptide but not to the non-phosphorylated form of the peptide or to other phosphopeptides, in a microtitre plate competition enzyme-linked immunosorbent assay. Anti-PS1327 antibody reacted well with native insulin receptor prepared from phorbol ester-treated transfected CHO.T cells, but showed little reaction with receptor from untreated cells. Anti-PT1348 antibody in crude form reacted substantially with receptor from both phorbol 12-myristate 13-acetate-treated and untreated cells, but displayed specificity for phosphoreceptor after adsorption to remove antibodies reactive with dephosphopeptide. The ability to discriminate between receptor from cells treated with or without phorbol ester was retained when these antibodies were used to probe denatured receptor on Western blots. Thus anti-PS1327 and anti-PT1348 react with insulin receptor in a site-specific and phosphorylation-state-dependent manner. Anti-PT1348, but not anti-PS1327, also showed increased reactivity with receptor prepared from insulin-treated cells. The third antibody, anti-PS1305, did not react with intact insulin receptor under any conditions. It is concluded that serine 1327 is a major, previously unrecognized, site of phorbol ester-induced receptor phosphorylation, and that anti-phosphopeptide antibodies will be valuable reagents with which to examine the serine/threonine phosphorylation state of receptor extracted from tissues.

Elevated protein tyrosine phosphatase activity and increased membrane viscosity are associated with impaired activation of the insulin receptor kinase in old rats

Insulin resistance is very common in the elderly, and may be associated with glucose intolerance or frank diabetes. In previous studies we demonstrated that insulin resistance in old Wistar rats is associated with decreased autophosphorylation and activation of the hepatic insulin receptor kinase (IRK) in vivo. We now show that this defect can be reproduced in vitro, where the extent of insulin-induced activation of IRK in liver membranes of old rats was decreased by approximately 50% compared with young controls. The defect could be largely abolished after solubilization of the membranes with Triton X-100. We also show that: (a) the viscosity of membranes from the old rats was significantly (P < 0.001, n = 4) higher (by 15%) compared with young controls; (b) incubation of plasma membranes from old animals with lecithin liposomes, which lowered their cholesterol levels, partially abolished the defect in IRK activation; and (c) Triton extracts of liver membranes prepared from old rats did not interfere with the activation of IRK derived from young controls. Additionally, non-membrane components did contribute to the development of this defect. We observed a significant (approximately 30%) (P < 0.001, n = 18) elevation of cytosolic protein tyrosine phosphatase (PTP) activity directed against the beta subunit of the insulin receptor in livers of old rats. No such elevation of PTP activity could be demonstrated with synthetic substrates. Our findings are consistent with a model in which increased membrane viscosity as well as enhancement of a cytosolic PTP activity both markedly inhibit the activation in vivo of the hepatic IRK in old animals.

Analysis of free and bound O-phosphoamino acids in urine by gas chromatography with flame photometric detection

A selective and sensitive method has been developed for the analysis of free and bound forms of O-phosphoamino acids, such as O-phosphoserine, O-phosphothreonine and O-phosphotyrosine, in urine samples by gas chromatography (GC). For free O-phosphoamino acid analysis, the urine sample was extracted with trichloroacetic acid and run through an ion exchange column. For total (free plus bound) O-phosphoamino acid analysis, the urine sample was hydrolysed in acid and base in order to release the O-phosphoamino acid from peptides or proteins. O-Phosphoamino acids in these prepared samples were converted into their N-isobutoxycarbonyl trimethyl ester derivatives and then measured by GC with flame photometric detection (FPD-GC). The calibration curve was linear in the range of 10-500 ng for each O-phosphoamino acid, and the detection limits were 30-80 pg as injection amounts. O-Phosphoamino acids in the urine samples could be selectively determined by the FPD-GC method without any influence from coexisting substances. The recoveries of O-phosphoamino acids added to urines and urine hydrolysates were 90-98% and relative standard deviations were 1.5-8.0%. By using this method, we investigated an age dependence of O-phosphoamino acid excretion in normal subjects.

Measurement of picomoles of phosphoamino acids by high-performance liquid chromatography

A reverse-phase, high-performance liquid chromatographic system (HPLC) is described that makes possible optimal resolution and quantitation of picomole levels of phosphoamino acids, both with or without the presence of a large excess of nonphosphorylated amino acids. The assay involves precolumn derivatization of an amino acid mixture with phenyl isothiocyanate (PITC) at room temperature, followed by separation of phosphoamino acids from other amino acids by HPLC. The liquid chromatography was carried out on a C18 reverse-phase column at pH 7.4 and 30 degrees C using gradient elution with eluent A as 157 mM sodium acetate containing 2% acetonitrile and eluent B as 60% acetonitrile in water. A uv absorption at 254 nm is employed for detection of the PITC-derivatized amino acids eluting from the column. Amino acids are eluted with baseline resolution in the following order: phosphoserine, phosphothreonine, aspartic acid, glutamic acid, and phosphotyrosine followed by other amino acids. The sensitivity is in the picomole range, and the separation time, injection to injection, is 36 min. Phosphoserine, phosphothreonine, and phosphotyrosine are resolved within the first 8 min. This procedure enables determination of as low as 5 pmol of nonradioactive phosphoamino acids in a 100-fold excess of amino acids, as is usually present in most phosphoproteins in the natural state. Phosphoamino acids in polypeptides separated by sodium dodecyl sulfate-polyacrylamide electrophoresis and transferred to polyvinylidene difluoride (PVDF) membrane, or protein samples directly blotted on the membrane, can also be analyzed by this procedure after acid hydrolysis of the proteins bound to the PVDF membrane.