Functional interrogation of the kinome using nucleotide acyl phosphates

The central role of protein kinases in signal transduction pathways has generated intense interest in targeting these enzymes for a wide range of therapeutic indications. Here we report a method for identifying and quantifying protein kinases in any biological sample or tissue from any species. The procedure relies on acyl phosphate-containing nucleotides, prepared from a biotin derivative and ATP or ADP. The acyl phosphate probes react selectively and covalently at the ATP binding sites of at least 75% of the known human protein kinases. Biotinylated peptide fragments from labeled proteomes are captured and then sequenced and identified using a mass spectrometry-based analysis platform to determine the kinases present and their relative levels. Further, direct competition between the probes and inhibitors can be assessed to determine inhibitor potency and selectivity against native protein kinases, as well as hundreds of other ATPases. The ability to broadly profile kinase activities in native proteomes offers an exciting prospect for both target discovery and inhibitor selectivity profiling.     

Magic angle sample spinning in inhomogeneously broadened biological systems

Recent advances in magic angle sample spinning experiments now permit observation of dilute spin high resolution n.m.r. spectra of arbitrary powder samples. In the 'slow-spinning' régime, for which the spinning rate is less than the size of the interaction that is being averaged, the spectra exhibit rotational side bands whose intensities contain information on chemical shift anisotropies. A technique for extracting shift anisotropies from side band intensities is discussed. Since many biologically interesting systems are solid or semi-solid in nature, this technique should find wide application to biological systems. Two illustrations of the point are given in this paper, namely, n.m.r. studies of membranes and of the phosphate-containing phases of bone.     

Cation bindint to alpha-sl-casein B. A comparison of electrostatic models.

System characteristics which determine calcium binding to and subsequent proton release from alpha-sl-casein B are reported at pH 6.6 and [Na-plus] equal to 0.04, 0.0, and 0.16M. Values of protein solvation, G, site bound calcium, Ca,S, and net monomer charge, Z, permitted distributed charge models to be constructed. The models examined proved inadequate in that it was impossible to keep the dielectric constant, D, within acceptable limits and/or predict measured proton release. Three discrete charge models were constructed. At D equals 4, all three gave good agreement between predicted and experimental data as Ca, S increased. The known amino acid sequence was used to make rodlet models for the whole molecule andfor just the phosphate-containing acidic peptide portion. A comparison of these shows the electrostatic dominance of the acidic peptide and suggests that the electrostatic environment for the remainder of the binding sites is essentially constant as Ca, S increases during addition of calcium ion. The third discrete charge model bends the acidic peptide rodlet into a torus. In this case, data were matched with less assumed bond strain under conditions of high molecular charge than with the other two models. This indicates that conformation and association may be important factors to consider when constructing discrete charge models to calculate electrostatic free energy.     

Determination of a putative phosphate-containing peptide in calreticulin.

Calreticulin is an abundant endo/sarcoplasmic reticulum (ER/SR) protein that may carry out multiple functions inside cells. Except for calreticulin, all of the major ER/SR Ca2+-binding proteins are substrates for protein kinase CK2 in vitro, which led us to hypothesize that native calreticulin might exist in the phosphorylated form. To investigate this possibility, we purified calreticulin from cardiac microsomes and verified its identity by immunoblot analysis and sequencing of tryptic peptides. Purified calreticulin, like cardiac calsequestrin, contained endogenous phosphate as determined by a Malachite green assay for phosphate. Previous analyses of cardiac calsequestrin have localized phosphate to a single tryptic peptide containing serine phosphate on sites phosphorylated by protein kinase CK2. Using a similar procedure, we analyzed calreticulin tryptic peptides with Malachite green, localizing phosphate binding to a single calreticulin peptide 367LKEEEEDKK. As this peptide contains no phosphorylatable residues, our results suggest that calreticulin may tightly bind phosphate or a phosphate-containing molecule at this site.     

A novel fluorometric assay for ADP-ribose pyrophosphatase activity

ADP-ribose pyrophosphatase (ADPRase) hydrolyzes ADP-ribose to ribose-5-phosphate and AMP. The ADPRase activity have been assessed by coupling the reaction to alkaline phosphatase and colorimetrically measuring the amount of inorganic phosphate released from AMP that is one of the products of ADPRase. Another but less sensitive colorimetric method has been employed: the reaction mixture was treated with charcoal to adsorb the adenine-containing compounds such as AMP and ADPR and subsequently remaining ribose-5-phosphate was measured colorimetrically. However, the measurement of inorganic phosphate cannot be feasible to assay ADPRase in phosphate-containing samples and the determination of ribose-5-phosphate also is less sensitive. Here we develop a fluorescent assay for ADPRase that utilizes 1, N(6)-etheno ADP-ribose, a fluorescent analogue of ADP-ribose. This method measures fluorescent 1, N(6)-etheno adenosine that is produced by coupling the hydrolysis of 1, N(6)-etheno ADP-ribose to dephosphorylation with alkaline phosphatase. The fluorometric assay is comparable in sensitivity and useful for ADPRase assay in phosphate-containing samples.     

Species-differentiable sensing of phosphate-containing anions in neutral aqueous solution based on coordinatively unsaturated lanthanide complex probes

A new chromogenic/fluorogenic molecular probe was developed for highly selective and species-differentiable detection of phosphate-containing anions in neutral aqueous solution. The coordinatively unsaturated lanthanide complex, made from Eu(III) ion and 2-[(8-hydroxy-5-sulfo-7-quinoline)azo]-1,8-dihydroxy-3,6-naphthalene disulfonic acid, changed its conformation when binding to the incoming target anions, which resulted in differential absorption or fluorescence responses. It was demonstrated that not only phosphate and pyrophosphate but also DNA and RNA could be clearly distinguished by visible absorption or fluorescence spectra. Also, differential responses in absorption spectra were observed when AMP, ADP, and ATP were added into the sensing system. Selective quantitation of these phosphate-containing anions in aqueous solutions, therefore, can be easily available. DNA and RNA were distinguished by different colors and independent fluorescence emissions due to their intrinsic differences in beta-D-ribose residues. Simultaneous or independent quantitation of DNA and RNA in a mixture sample, therefore, is possible without pretreatment with nuclease. Furthermore, the influence from the base selectivity can be eliminated by the use of the probe. The detection limits of phosphate and 5'-ATP in neutral water were 6.0 x 10(-7) and 9.0 x 10(-7)M, respectively, by the UV/Vis spectrophotometric method; the detection limits were 12.3 ng/mL for DNA by fluorimetry and 2.3mg/L for RNA by UV/Vis spectrophotometry.     

A rapid method for the determination of glycerophosphorylcholine in rabbit and bull seminal plasma

Glycerophosphorylcholine is the only phosphate-containing compound of bull or rabbit seminal plasma that is eluted by water from a semimicro column of Dowex 1-acetate. This observation has permitted development of a rapid method for glycerophosphorylcholine analysis.     

Rapid identification of proteins by peptide-mass fingerprinting

BACKGROUND: Developments in 'soft' ionisation techniques have revolutionized mass-spectro-metric approaches for the analysis of protein structure. For more than a decade, such techniques have been used, in conjuction with digestion b specific proteases, to produce accurate peptide molecular weight 'fingerprints' of proteins. These fingerprints have commonly been used to screen known proteins, in order to detect errors of translation, to characterize post-translational modifications and to assign diulphide bonds. However, the extent to which peptide-mass information can be used alone to identify unknown sample proteins, independent of other analytical methods such as protein sequence analysis, has remained largely unexplored. RESULTS: We report here on the development of the molecular weight search (MOWSE) peptide-mass database at the SERC Daresbury Laboratory. Practical experience has shown that sample proteins can be uniquely identified from a few as three or four experimentally determined peptide masses when these are screened against a fragment database that is derived from over 50 000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, thus permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino-acid composition or linear sequence, peptide masses provide a set of determinants that are sufficiently discriminating to identify or match unknown sample proteins. CONCLUSION: Peptide-mass fingerprints can prove as discriminating as linear peptide sequences, but can be obtained in a fraction of the time using less protein. In many cases, this allows for a rapid identification of a sample protein before committing it to protein sequence analysis. Fragment masses also provide information, at the protein level, that is complementary to the information provided by large-scale DNA sequencing or mapping projects.     

Antithrombin action of phosvitin and other phosphate-containing polyanions is mediated by heparin cofactor II

We have examined the antithrombin effects of various phosphate-containing polyanions (including linear polyphosphates, polynucleotides and the phosphoserine glycoprotein, phosvitin) on the glycosaminoglycan-binding plasma proteinase inhibitors, antithrombin III (ATIII) and heparin cofactor II (HCII). These phosphate-containing polyanions accelerate the HCII-thrombin reaction, as much as 1600-fold in the case of phosvitin. The HCII-thrombin reaction with both phosvitin and polynucleotides appears to follow the ternary complex mechanism. The HCII-thrombin complex is rapidly formed in the presence of these phosphate polyanions (each at 10 micrograms/ml) when 125I-labeled thrombin is incubated with human plasma (ex vivo). None of these phosphate polyanions accelerate the ATIII-thrombin reaction. Our results suggest that the antithrombotic effect of these phosphate-containing polyanions is mediated by HCII activation and not by ATIII.     

Specificity and structural analysis of a guinea pig transfer factor-like activity.

A transfer factor-like activity was prepared by Sephadex G-25 chromatography of immune guinea pig leukocyte lysates. This isolated material leads to antigen-dependent migration inhibition and thymidine uptake by nonimmune lymphoid cells. Tests of the "transfer factor" from guinea pigs immunized to either ovalbumin or bovine gamma-globulin demonstrated the donor specificity of the in vitro activity. The activity is susceptible to heat (56 degrees C), alkali (0.5 M sodium hydroxide), pronase, and phosphodiesterase. The pronase susceptibility is blocked by traysylol, a protease inhibitor; the phosphodiesterase susceptibility is not bocked by traysylol. The guinea pig factor was purified further by alkaline phosphatase treatment. Sephadex G-25 chromatography, and DEAE-cellulose chromatography. The final product, active in vitro, represents about 0.03% of the cellular material absorbing 260 nm light, and contains polymerized amines and phosphate. Gel electrophoresis of the fluram-reactive components suggests a limited heterogeneity of the DEAE-cellulose-purified material. These data are consistent with the active "transfer factor" molecule including both peptide and phosphate-containing components.     

A rapid and sensitive method for the identification and quantitation of sub-picomolar amounts of neurohypophysial peptides

A simple, rapid and sensitive method, using isocratic reversed-phase HPLC, is described for the concomitant identification and quantitation of low levels of the various neurohypophysial peptides in biological tissues and fluids. The method requires little or no sample preparation and utilises UV peak detection at 215 nm with a serial signal amplification system to achieve a usable maximum sensitivity of less than 200 fmol of peptide.     

Enzymatic activities in cultured human lymphocytes that dephosphorylate dolichyl pyrophosphate and dolichyl phosphate

Enzymatic activities which dephosphorylate dolichyl phosphate (Dol-P) and dolichyl pyrophosphate (Dol-P-P) have been observed in membranes from cultured human lymphocytes. Neither activity requires divalent metals. Dol-P phosphatase is inhibited by inorganic phosphate but not by other phosphate-containing compounds. Dol-P-P phosphatase is inhibited by bacitracin but not by phosphate-containing compounds including the methylene analogue of pyrophosphate. These reactions are similar to those previously found in the cycle of bacterial wall peptidoglycan biosynthesis. A chemical synthesis of [32P]Dol-P and [32P]Dol-P-P is reported.     

An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 +/- 0.025 M-1 min-1. Inactivation by pyridoxal 5'-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7700 +/- 860 M-1 min-1. A second-order rate constant of inactivation for the irreversible reaction catalyzed by the enzyme is 1434 +/- 110 M-1 min-1. Treatment of the enzyme with pyridoxal 5'-phosphate gives incorporation of 1 mol of pyridoxal 5'-phosphate per mole of enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of kobs vs pH suggests this active-site lysine has a pKa of 8.1 and a pH-independent rate constant of inactivation of 47,700 M-1 min-1. The phosphate-containing substrates IDP, ITP, and phosphoenolpyruvate offer almost complete protection against inactivation by pyridoxal 5'-phosphate. Modified, inactive enzyme exhibits little change in Mn2+ binding as shown by EPR. Proton relaxation rate measurements suggest that pyridoxal 5'-phosphate modification alters binding of the phosphate-containing substrates. 31P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme.Mn2+.substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5'-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.     

Development of a novel ectonucleotidase assay suitable for high-throughput screening

5'-Ectonucleotidase (NT5E) catalyzes the conversion of adenosine monophosphate to adenosine and free phosphate. The role of this ectonucleotidase and its production of adenosine are linked with immune function, angiogenesis, and cancer. NT5E activity is typically assayed either by chromatographic quantification of substrates and products using high-performance liquid chromatography (HPLC) or by quantification of free phosphate using malachite green. These methods are not suitable for robust screening assays of NT5E activity. HPLC is not readily suitable for the rapid and efficient assay of multiple samples and malachite green is highly sensitive to the phosphate-containing buffers common in various media and sample buffers. Here the development and validation of a novel high-throughput ectonucleotidase screening assay are described, which makes use of a luciferase-based assay reagent, the Promega CellTiter-Glo kit, to measure the catabolism of AMP by NT5E. This multiwell plate-based assay facilitates the screening of potential ectonucleotidase antagonists and is unaffected by the presence of contaminating phosphate molecules present in screening samples.     

Design and function of a conformationally restricted analog of the influenza virus fusion peptide.

A conformationally restricted analog of the N-terminal 12-residue peptide segment of the HA2 subunit of the PPV/34, PR/8/34, and Jap/57 strains of influenza virus hemagglutinin was synthesized containing three residues of Calpha-methyl-valine. This peptide has a higher content of helical structure in the presence of 50% trifluoroethanol or when interacting with liposomes of egg phosphatidylcholine compared with the conformationally more flexible control peptide with the native sequence. The control and analog peptides had opposite effects on membrane curvature as measured by shifts in the bilayer-to-hexagonal phase transition temperature of a synthetic phosphatidylethanolamine derivative. The control peptide promoted more negative curvature, particularly at acidic pH and was also more potent than the analog in promoting lipid mixing. The results indicate that the ability of the peptide to sample a broader range of conformations is required for the influenza fusion peptide to destabilize membranes and that a rigid helical structure is less fusogenic. The difference between the two peptides and between pH 7.4 and pH 5.0 show a correlation between the ability to promote negative curvature and to accelerate lipid mixing.     

SWATH enables precise label‐free quantification on proteome scale

MS‐based proteomics has emerged as a powerful tool in biological studies. The shotgun proteomics strategy, in which proteolytic peptides are analyzed in data‐dependent mode, enables a detection of the most comprehensive proteome (>10 000 proteins from whole‐cell lysate). The quantitative proteomics uses stable isotopes or label‐free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label‐free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. Sequential window acquisition of all theoretical mass spectra (SWATH) is a recently developed technique, in which data‐independent acquisition is coupled with peptide spectral library match. In principle SWATH method is able to do label‐free quantification in an MRM‐like manner, which has higher quantification accuracy and precision. Previous data have demonstrated that SWATH can be used to quantify less complex systems, such as spiked‐in peptide mixture or protein complex. Our study first time assessed the quantification performance of SWATH method on proteome scale using a complex mouse‐cell lysate sample. In total 3600 proteins got identified and quantified without sample prefractionation. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly. However, this inaccuracy does not prevent discovering biological correlates, because the measured signal intensities had linear relationship to the sample loading amounts; thus the SWATH method can predict precisely the significance of a protein. Our results prove that SWATH can provide precise label‐free quantification on proteome scale.     

Bottom‐up proteome analysis of E. coli using capillary zone electrophoresis‐tandem mass spectrometry with an electrokinetic sheath‐flow electrospray interface

The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE‐ESI‐MS/MS. The separation was performed in a 60‐cm‐long linear polyacrylamide‐coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath‐flow electrospray interface was used to couple the separation capillary with an Orbitrap‐Velos operating in higher‐energy collisional dissociation mode. Each CZE‐ESI‐MS/MS run lasted 50 min and total MS time was 350 min. A total of 23 706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom‐up analysis of prokaryote proteomes.     

A model of tissue thromboplastin

The molecular structure of the human brain tissue thromboplastin was studied by the method of NMR-31P and 1H using the shifting reagent. Molecular model of the tissue thromboplastin is suggested. According to the model only 10-20% of polar phosphate-containing heads are exposed outside. Phospholipids located deeper form hexagonal (HII) cylinders which may consist only of lipids or of complexes with proteins.     

Amino acid analysis of peptide loading ratios in conjugate vaccines: a comparison of direct electrochemical detection and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate pre-column derivatization methods

Amino acid analysis using direct electrochemical detection was compared with precolumn fluorescent derivatization using 6-aminoquinolyl- N-hydroxysuccinimidyl carbamate (AQC) for evaluation of the degree of covalent coupling of peptides to a carrier-protein complex derived from the bacteria Neisseria meningitidis. AQC derivatization was found to give superior sensitivity compared to electrochemical detection, with less interference from sample components such as carbohydrates or buffer salts. Hydrolysis time and temperature were optimized for maximal recoveries of the marker amino acid 6-aminohexanoic acid (epsilon-Ahx) and the unique amino acids S-dicarboxyethyl cysteine (SDCEC) and S-carboxymethyl homocysteine (SCHMC), which are generated upon the hydrolysis of the covalent linkage between the peptide and the carrier protein. Quantitation of these amino acids enabled the determination of the ratio of peptide to protein in the conjugate samples.     

Accumulation of phosphate-containing granules in the nucleoid area of Pseudomonas aeruginosa

Many electron-dense granules were found in the nucleoid area of Pseudomonas aeruginosa strain K by electron microscopy with the technique of the freeze-substitution method. These granules contained phosphorus and calcium as determined by X-ray microanalysis. The size and the numbers of the granules decreased when the bacteria was cultured in the medium from which phosphate-containing compounds were depleted. From these observations we concluded that the granule was a phosphate-containing granule and possibly a polyphosphate granule. The excellent preservation of the fine structures by the freeze-substitution technique enables us to show very small polyphosphate granules in the nucleoid area of the bacterial cells which cannot be revealed by the conventional chemical fixation method. As we could not see the granules in other bacteria cultured in nutrient medium such as Serratia, Escherichia, Bacillus and Vibrios, the accumulation of the phosphate granules in Ps. aeruginosa might be a unique character of this bacteria and might be related to the growing capability of this bacteria in extremely low nutrient supply.