Applications of mass spectrometry to signal transduction

Probing the molecular basis for potent and selective protein-tyrosine phosphatase 1B inhibition

Protein-tyrosine phosphatases (PTPs) are important for the control of proper cellular tyrosine phosphorylation. Despite the large number of PTPs encoded in the human genome and the emerging roles played by PTPs in human diseases, a detailed understanding of the role played by PTPs in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific inhibitors. Such inhibitors could serve as useful tools for determining the physiological functions of PTPs and may constitute valuable therapeutics in the treatment of several human diseases. However, because of the highly conserved nature of the active site, it has been difficult to develop selective PTP inhibitors. By taking an approach to tether together two small ligands that can interact simultaneously with the active site and a unique proximal noncatalytic site, we have recently acquired Compound 2 (see Fig. 1), the most potent and selective PTP1B inhibitor identified to date, which exhibits several orders of magnitude selectivity in favor of PTP1B against a panel of PTPs. We describe an evaluation of the interaction between 2 and its analogs with PTP1B and its site-directed mutants selected based on hydrogen/deuterium exchange of PTP1B backbone amides in the presence and absence of 2. We have established the binding mode of Compound 2 and identified 12 PTP1B residues that are important for the potency and selectivity of Compound 2. Although many of the residues important for Compound 2 binding are not unique to PTP1B, the combinations of all contact residues differ between PTP isozymes, which suggest that the binding surface defined by these residues in individual PTPs determines inhibitor selectivity. Our results provide structural information toward understanding of the molecular basis for potent and selective PTP1B inhibition and further establish the feasibility of acquiring potent, yet highly selective, PTP inhibitory agents.

Analysis of signaling pathways using functional proteomics

Advances in analytical methods for protein analysis by mass spectrometry provide new tools for global analysis of the expressed protein profile of cells (referred to as proteomics). Currently, available methodology samples only part of the proteome. This is sufficient for analysis of signal transduction, because signaling pathways contain enzymes, which modify high-abundance proteins other than those of the pathway. Thus, modulation of the signaling through a pathway will produce a "footprint" in the proteome that is characteristic of a specific cell phenotype. Comparison of different samples to identify these differences in posttranslational modification or protein expression is referred to as functional proteomics. This review surveys the methods in widest use in functional proteomics, as well as a few promising new ones. Although proteomic analyses were first conducted 26 years ago, a renewed interest is fueled by several recent advances. Most important are the availability of public genome and protein databases and the development of high-sensitivity, easy-to-use mass spectrometers and database search engines capable of exploiting these databases. Other important advances include improved two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), computer programs for analysis of the 2D-PAGE gel images, protocols for proteolytic digestion of proteins in excised gel pieces, and low-flow chromatography methods. Despite the limitations of these methods, they can distinguish subtle changes in the phenotype of cells, providing the basis for future studies in regulation of the phenotype.

A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate

Although proteins phosphorylated on tyrosine residues can be enriched by immunoprecipitation with anti-phosphotyrosine antibodies, it has been difficult to identify proteins that are phosphorylated on serine/threonine residues because of lack of immunoprecipitating antibodies. In this report, we describe several antibodies that recognize phosphoserine/phosphothreonine-containing proteins by Western blotting. Importantly, these antibodies can be used to enrich for proteins phosphorylated on serine/threonine residues by immunoprecipitation, as well. Using these antibodies, we have immunoprecipitated proteins from untreated cells or those treated with calyculin A, a serine/threonine phosphatase inhibitor. Mass spectrometry-based analysis of bands from one-dimensional gels that were specifically observed in calyculin A-treated samples resulted in identification of several known serine/threonine-phosphorylated proteins including drebrin 1, alpha-actinin 4, and filamin-1. We also identified a protein, poly(A)-binding protein 2, which was previously not known to be phosphorylated, in addition to a novel protein without any obvious domains that we designate as Frigg. Frigg is widely expressed and was demonstrated to be a protein kinase A substrate in vitro. We identified several in vivo phosphorylation sites by tandem mass spectrometry using Frigg protein immunoprecipitated from cells. Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways.

Global regulation of post-translational modifications on core histones

Full-length masses of histones were analyzed by mass spectrometry to characterize post-translational modifications of bulk histones and their changes induced by cell stimulation. By matching masses of unique peptides with full-length masses, H4 and the variants H2A.1, H2B.1, and H3.1 were identified as the main histone forms in K562 cells. Mass changes caused by covalent modifications were measured in a dose- and time-dependent manner following inhibition of phosphatases by okadaic acid. Histones H2A, H3, and H4 underwent changes in mass consistent with altered acetylation and phosphorylation, whereas H2B mass was largely unchanged. Unexpectedly, histone H4 became almost completely deacetylated in a dose-dependent manner that occurred independently of phosphorylation. Okadaic acid also partially blocked H4 hyperacetylation induced by trichostatin-A, suggesting that the mechanism of deacetylation involves inhibition of H4 acetyltransferase activity, following perturbation of cellular phosphatases. In addition, mass changes in H3 in response to okadaic acid were consistent with phosphorylation of methylated, acetylated, and phosphorylated forms. Finally, kinetic differences were observed with respect to the rate of phosphorylation of H2A versus H4, suggesting differential regulation of phosphorylation at sites on these proteins, which are highly related by sequence. These results provide novel evidence that global covalent modifications of chromatin-bound histones are regulated through phosphorylation-dependent mechanisms.

Investigations of the lysophospholipid composition of human neutrophils under different stimulation conditions by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Matrix-assisted laser desorption / ionization time-of-flight mass spectrometry (MALDI-TOF MS) is usually used for the analyses of proteins carbohydrates and oligonucleotides. In spite of the number of advantages that MALDI-TOF MS exhibits for lipid analysis, this method has not often been applied in this field. In this paper we have extended our previous studies on the suitability of MALDI-TOF MS for the investigation of changes in the content of lipid-derived second messengers in organic extracts of human neutrophils. Qualitative differences in the lysophospholipid composition in organic extracts of the human neutrophils under different stimulation conditions could be easily observed by MALDI-TOF MS. Although there are still some methodological problems to be solved before this method can be routinely applied for the quantification of different lipid classes in complex biological mixtures (such as organic extracts of human neutrophils) it is shown here that MALDI-TOF MS possesses the capability to be used as a simple screening method for the investigation of the content of lipid-derived second messengers and of signalling pathways in cells.

Enhanced prediction accuracy of protein secondary structure using hydrogen exchange Fourier transform infrared spectroscopy

A novel equilibrium hydrogen exchange Fourier transform IR (HX-FTIR) spectroscopy method for predicting secondary structure content was employed using spectra obtained for a training set of 23 globular proteins. The IR bandshape and frequency changes resulting from controlled levels of H-D exchange were observed to be protein-dependent. Their analysis revealed these variations to be partly correlated to secondary structure. For each protein, a set of 6 spectra was measured with a systematic variation of the solvent H-D ratio and was subjected to factor analysis. The most significant component spectra for each protein, representing independent aspects of the spectral response to deuteration, were each subjected to a second factor analysis over the entire training set. Restricted multiple regression (RMR) analysis using the loadings of the principal components from 19 of these H-D analyses revealed an improvement in prediction accuracy compared with conventional bandshape-based analyses of FTIR data. Nearly a factor of 2 reduction in error for prediction of helix fractions was found using s1, the average spectral response for the H-D set. In some cases, significant error reduction for prediction of minor components was found using higher factors. Using the same analytical methods, prediction errors with this new deuteration-response-FTIR method were shown to be even better than those obtained by use of electronic circular dichroism (ECD) data for helix predictions and to be significantly lower for ECD-based sheet prediction, making these the best secondary structure predictions obtained with the RMR method. Tests of a limited variable selection scheme showed further improvements, consistent with previous results of this approach using ECD data.