Peptides from myelin basic protein as substrates for adenosine 3', 5'-cyclic monophosphate-dependent protein kinases

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification

Constitutive activation of one or more kinase signaling pathways is a hallmark of many cancers. Here we extend the previously described mass spectrometry-based KAYAK approach by monitoring kinase activities from multiple signaling pathways simultaneously. This improved single-reaction strategy, which quantifies the phosphorylation of 90 synthetic peptides in a single mass spectrometry run, is compatible with nanogram to microgram amounts of cell lysate. Furthermore, the approach enhances kinase monospecificity through substrate competition effects, faithfully reporting the signatures of many signaling pathways after mitogen stimulation or of basal pathway activation differences across a panel of well-studied cancer cell lines. Hierarchical clustering of activities from related experiments groups peptides phosphorylated by similar kinases together and, when combined with pathway alteration using pharmacological inhibitors, distinguishes underlying differences in potency, off-target effects and genetic backgrounds. Finally, we introduce a strategy to identify the kinase, and even associated protein complex members, responsible for phosphorylation events of interest.

Nonphosphorylatable tyrosine surrogates. Implications for protein kinase inhibitor design

Tyrosine-specific protein kinases are known to utilize short synthetic tyrosine-containing peptides as substrates and, as a consequence, a number of inhibitory peptides have been prepared by replacing the tyrosine moiety in these peptides with a nonphosphorylatable phenylalanine residue. Unfortunately, the inhibitory efficacy of these phenylalanine-based peptides is often disappointing. These results demonstrate the need for nonphosphorylatable tyrosine surrogates that enhance enzyme affinity. As a consequence, we prepared nearly two dozen different phenethylamine derivatives, attached them to the C terminus of an active site-directed peptide (Glu-Glu-Leu-Leu), and examined their effectiveness as inhibitors of pp60(c-)src. Three derivatives exhibit enhanced inhibitory activity (relative to phenethylamine), including para-substituted sulfonamide and guanidino analogs as well as a pentafluoro-containing species. The para-sulfonamide derivative was selected for further study and was found to function as a competitive inhibitor versus variable peptide substrate and as a noncompetitive inhibitor versus variable ATP. In short, the enhanced inhibitory activity of the sulfonamide derivative is not due to the association of this moiety with the ATP binding site. Furthermore, peptides containing the para-guanidino and pentafluoro derivatives of phenylalanine were prepared. These species also display enhanced inhibitory activity toward pp60(c-)src relative to the corresponding phenylalanine-based peptide.

Animal membrane receptors and adhesive molecules

This review summarizes some important data, principles, opinions, commentaries, and modern methodology concerning the receptor structure, interactions, signaling and receptor-mediated cell functions. Three sections give a brief overview of the signaling synergy, multivariant signaling, and some reactions in phosphorylation networks. A concise report about the cytotoxic reaction of NK cells represents an example of multistage recognition reaction, involving differently acting receptors, changes in affinities of cell-cell interactions, and secretion of regulatory and cytotoxic molecules. Some interesting trends in receptor engineering, including antibody molecules as a special receptor phenomenon are mentioned in the final section.

Substrate and pseudosubstrate interactions with protein kinases: determinants of specificity

Protein crystallography has revealed that protein kinases have extended protein-substrate-binding grooves associated with their active sites. Some protein kinases are autoinhibited by a mechanism in which part of their structure, termed a pseudosubstrate, occupies the active site. Substrates and pseudosubstrates occupy overlapping regions within the extended substrate-binding groove, making multiple specific electrostatic and non-polar contacts. With masterly economy, Nature has exploited the active site in many protein kinases to both recognize substrates with great specificity and autoregulate by remaining inactive until the appropriate activation signal is received.

Identification of phosphorylation sites for adenosine 3',5'-cyclic phosphate dependent protein kinase on the voltage-sensitive sodium channel from Electrophorus electricus

The voltage-sensitive sodium channel from the electroplax of Electrophorus electricus is selectively phosphorylated by the catalytic subunit of cyclic-AMP-dependent protein kinase (protein kinase A) but not by protein kinase C. Under identical limiting conditions, the protein was phosphorylated 20% as rapidly as the synthetic model substrate kemptamide. A maximum of 1.7 +/- 0.6 equiv of phosphate is incorporated per mole. Phosphoamino acid analysis revealed labeled phosphoserine and phosphothreonine at a constant ratio of 3.3:1. Seven distinct phosphopeptides were identified among tryptic fragments prepared from radiolabeled, affinity-purified protein and resolved by HPLC. The three most rapidly labeled fragments were further purified and sequenced. Four phosphorylated amino acids were identified deriving from three consensus phosphorylation sites. These were serine 6, serine 7, and threonine 17 from the amino terminus and a residue within 47 amino acids of the carboxyl terminus, apparently serine 1776. The alpha-subunits of brain sodium channels, like the electroplax protein, are readily phosphorylated by protein kinase A. However, these are also phosphorylated by protein kinase C and exhibit a markedly different pattern of incorporation. Each of three brain alpha-subunits displays an approximately 200 amino acid segment between homologous repeat domains I and II, which is missing from the electroplax and skeletal muscle proteins [Noda et al. (1986) Nature (London) 320, 188; Kayano et al. (1988) FEBS Lett. 228, 1878; Trimmer et al. (1989) Neuron 3, 33]. Most of the phosphorylation of the brain proteins occurs on a cluster of consensus phosphorylation sites located in this segment. This contrasts with the pattern of highly active sites on the amino and carboxyl termini of the electroplax protein. The detection of seven labeled tryptic phosphopeptides compared to the maximal labeling stoichiometry of approximately 2 suggests that many of the acceptor sites on the protein may be blocked by endogenous phosphorylation.

Protein kinase assay by paper-trichloroacetic acid method: high performance using phosphocellulose paper and washing an ensemble of samples on flat sheets

Phosphocellulose paper has been found to be the paper of choice in assaying protein kinase activities using [gamma-32P]ATP by the trichloroacetic acid method of precipitation and washing. A study of binding of ATP of increasing concentrations at constant specific activity with Whatman 3MM or ATP-coated Whatman 3 MM papers (in vogue) versus phosphocellulose paper (proposed here) has shown that the latter has the least affinity for ATP when washing is done with either trichloracetic acid or trichloroacetic acid containing pyrophosphate. In an experiment where the placental cytosolic protein kinase was serially diluted, the phosphocellulose paper was found to give higher signal/noise ratios at all dilutions studied compared to the other two papers. With regard to the technological side of washing the papers, we have found that the traditional method of cutting papers into small squares before loading the samples is perhaps not the best. Instead, we propose the use of a flat sheet matrix for loading the samples because this method ensures uniformity of washing among the samples while shaking is performed on a simple shaker. In addition, the whole paper matrix can provide an almost instantaneous autoradiogram of hundreds of samples facilitating biochemical experimentation with protein kinases.

Fluorometric assay for adenosine 3',5'-cyclic monophosphate-dependent protein kinase and phosphoprotein phosphatase activities

A novel peptide substrate for adenosine 3',5'-cyclic monophosphate-dependent protein kinase (ATP:protein phosphotransferase, EC 2.7.1.37), Leu-Arg-Arg-Trp-Ser-Leu-Gly, was synthesized. Phosphorylation of the peptide causes a 20% increase in the peptide fluorescence intensity at 358 nm. Values of Km and kcat for the phosphorylation reaction at pH 7.0 (25 degrees C), were determined to be 2.7 +/- 0.5 microM and 5.5 +/- 0.4 sec-1, respectively. The phosphorylated peptide was shown to be an effective substrate for phosphoprotein phosphatase (phosphoprotein phosphohydrolase, EC 3.1.3.16) with a Km of 113 +/- 10 microM and a kcat of 2.4 +/- 0.2 sec-1 in the presence of 2.5 mM MnCl2. Changes in the peptide fluorescence intensity as a function of its phosphorylation state provide a highly sensitive assay of cyclic AMP-dependent protein kinase and phosphoprotein phosphatase activities.

Amino acid sequence around the phosphorylated sites of porcine and rat liver pyruvate kinase, type L

Chymotrypsin removed the phosphorylated site of porcine liver pyruvate kinase without inactivating the enzyme. The amino acid sequence of the phosphopeptide obtained was analyzed. By analysis of CNBr fragments containing 33 amino acid residues, further information was obtained on the amino acid sequence around the phosphorylated sites of porcine and rat liver pyruvate kinase. It was found to be (formula see text) for the porcine isozyme and was very similar for the rat isozyme, although the order of the five most C-terminal amino acid residues (Leu, Pro, Ala2, Homoserine) in this fragment was not resolved and Leu was exchanged for Val in position 12 and Arg for Gln in position 26. The chymotryptic porcine isozyme phosphopeptide, composed of 18 amino acid residues, was entirely contained in the corresponding CNBr fragment (residues 7-24).

Phosphorylated sites in substrates of intracellular protein kinases: a common feature in amino acid sequences

Examination of the primary amino acid sequences surrounding phosphorylated sites in many intracellular phosphoproteins indicated that the phosphorylated hydroxyamino acid (either serine or threonine) is, in general, surrounded by amino acids having a positively charged side chain and, more specifically, is frequently separated from a basic amino acid (either lysine or arginine) by only one amino acid. Possible reasons for this common feature are discussed.

Substrate specificity of the cyclic AMP-dependent protein kinase

The protein substrate specificity of the catalytic subunit of rabbit skeletal muscle cyclic AMP-dependent protein kinase (EC 2.7.1.37; ATP:protein phosphotransferase) has been studied using genetic variants of beta casein. It was found that beta casein-B was phosphorylated at a much greater rate than beta caseins A1, A2, A3, or C. The enhanced phosphorylation of beta casein-B, as compared with the most common variant A2, was attributed to an arginine substitution for a serine at position 122, which caused a nearby residue, serine 124, to become a phosphorylation site for the protein kinase. These results further support the concept that the local primary structure is important in specificity and that arginine may be a specific determinant common to all the local phosphorylation site sequences recognized by the cyclic AMP-dependent protein kinase.