Design of a bacterial host for site-specific incorporation of p-bromophenylalanine into recombinant proteins

Introduction of a yeast suppressor tRNA (ytRNA(Phe)(CUA)) and a mutant yeast phenylalanyl-tRNA synthetase (yPheRS (T415G)) into an Escherichia coli expression host allows in vivo incorporation of phenylalanine analogues into recombinant proteins in response to amber stop codons. However, high-fidelity incorporation of non-natural amino acids is precluded in this system by mischarging of ytRNA(Phe)(CUA) with tryptophan (Trp) and lysine (Lys). Here we show that ytRNA(Phe)(CUA) and yPheRS can be redesigned to achieve high-fidelity amber codon suppression through delivery of p-bromophenylalanine (pBrF). Two strategies were used to reduce misincorporation of Trp and Lys. First, Lys misincorporation was eliminated by disruption of a Watson-Crick base pair between nucleotides 30 and 40 in ytRNA(Phe)(CUA). Loss of this base pair reduces mischarging by the E. coli lysyl-tRNA synthetase. Second, the binding site of yPheRS was redesigned to enhance specificity for pBrF. Specifically, we used the T415A variant, which exhibits 5-fold higher activity toward pBrF as compared to Trp in ATP-PP(i) exchange assays. Combining mutant ytRNA(Phe)(CUA) and yPheRS (T415A) allowed incorporation of pBrF into murine dihydrofolate reductase in response to an amber codon with at least 98% fidelity.     

Synthesis and characterization of p-phenylenediamine derivatives bearing an electron-acceptor unit

[reaction: see text] Two series of aniline oligomers bearing fused heterocycles as an electron-acceptor unit were synthesized. They consist of aniline or its derivatives as an electron donor and benzothiadiazole (BT) or quinoxaline (QX) as an electron-acceptor unit. Benzothiadiazoles 1-3 were synthesized by palladium-catalyzed amination. Quinoxalines 4-6 were prepared by palladium-catalyzed amination or transformation from the benzothiadiazoles. These compounds showed a HOMO-LUMO gap smaller than those of their analogues such as thiophene-substituted BT/QXs. Cyclic voltammetry revealed that the electrochemical behavior is dependent on the position of the acceptor heterocycle. Chemical oxidation with Ag2O afforded the corresponding 1,4-quinonediimine derivatives as an E,E-isomer, stereoselectively. As for the BT pentamer analogues 2 and 3, the first oxidation selectively occurred at the amino group adjacent to the benzothiadiazole unit, giving the regiospecific half-oxidized derivatives. Furthermore, the fully oxidized derivative 24 was isolated and characterized.     

Unexpected preference of the E. coli translation system for the ester bond during incorporation of backbone-elongated substrates

There have been recent advances in the ribosomal synthesis of various molecules composed of nonnatural ribosomal substrates. However, the ribosome has strict limitations on substrates with elongated backbones. Here, we show an unexpected loophole in the E. coli translation system, based on a remarkable disparity in its selectivity for beta-amino/hydroxy acids. We challenged beta-hydroxypropionic acid (beta-HPA), which is less nucleophilic than beta-amino acids but free from protonation, to produce a new repertoire of ribosome-compatible but main-chain-elongated substrates. PAGE analysis and mass-coupled S-tag assays of amber suppression experiments using yeast suppressor tRNAPheCUA confirmed the actual incorporation of beta-HPA into proteins/oligopeptides. We investigated the side-chain effects of beta-HPA and found that the side chain at position alpha and R stereochemistry of the beta-substrate is preferred and even notably enhances the efficiency of incorporation as compared to the parent substrate. These results indicate that the E. coli translation machinery can utilize main-chain-elongated substrates if the pKa of the substrate is appropriately chosen.     

Nucleotide sequence of aminoglycoside 6'-N-acetyltransferase [AAC(6')] determinant from Serratia sp. 45.

Gene for aminoglycoside 6'-N-acetyltransferase [AAC(6')] from Serratia sp. 45 was cloned into E. coli. The enzyme produced in E. coli carrying the recombinant plasmid was compared to the Serratia enzyme. Both enzymes acetylated the 6'-C position of amikacin, dibekacin, tobramycin, sisomicin, gentamicin C1a and kanamycin but effected gentamicin C1, gentamicin C2 and micronomycin minimally. No significant difference in optimal pH, isoelectric point or molecular weight was detected. The nucleotide sequence of the gene was determined. Initiating with a GTG codon for methionine, it was composed of 552 base pair coding for 184 amino acids. The molecular weight of the enzyme was about 20418. Comparison of the amino acid sequence of this AAC(6') with the amino acid sequence of aacA4 gene from Serratia marcescens (G. Tran Van Nhieu and E. Collatz, J. Bacteriol., 169, 5708(1987)) showed 98.3% homology.     

Cell transport via electromigration in polymer-based microfluidic devices

Electrokinetic transport of Escherichia coli and Saccharomyces cerevisiae (baker's yeast) cells was evaluated in microfluidic devices fabricated in pristine and UV-modified poly(methyl methacrylate)(PMMA) and polycarbonate (PC). Chip-to-chip reproducibility of the cell's apparent mobilities (micro(app)) varied slightly with a RSD of approximately 10%. The highest micro(app) for baker's yeast cells was observed in UV-modified PC with 0.5 mM PBS (pH = 7.4), and the lowest was measured in pristine PMMA with 20 mM PBS (pH = 7.4). Baker's yeast in all devices migrated toward the cathode because of their smaller electrophoretic mobility compared to the EOF. In 0.5 mM and 1 mM PBS, E. coli cells migrated toward the anode in all cases, opposite to the direction of the EOF due to their larger electrophoretic mobility. E. coli cells in 20 mM PBS migrated toward the cathode, which indicated that the electrophoretic mobility of E. coli cells decreased at higher ionic strengths. Observed differential migrations of E. coli and baker's yeast cells in appropriately prepared polymer microchips were used as the basis for selective introduction into microfluidic devices of only one type of cell. As a working model, experiments were performed with E. coli and RBCs (red blood cells). RBCs migrated toward the cathode in pristine PMMA with 1 mM and 20 mM PBS (pH = 7.4), opposite to the direction of the E. coli cells. By judicious choice of the buffer concentration in which the cell suspension was prepared and the polymer material, RBCs or E. coli cells were selectively introduced into the microdevice, which was monitored via laser backscatter signals.     

A new way to understand quaternary structure changes of hemoglobin upon ligand binding on the basis of UV-resonance Raman evaluation of intersubunit interactions

The single residue vibrational spectra of tryptophan (Trp) and tyrosine (Tyr) residues in human adult hemoglobin (HbA), which play important roles in cooperative oxygen binding, were determined for the deoxy and CO-bound forms by applying UV resonance Raman spectroscopy to various variant Hbs. It was found that Trpβ37, Tyrα42, Tyrα140, and Tyrβ145 at the α(1)-β(2) subunit interface underwent transitions between two contact states (named as T and R) upon ligand binding, while Trpα14, Trpβ15, and Tyrβ35 displayed little changes. The corresponding spectral changes were identified only for the α(2)β(2) tetramer, but not the isolated α and β chains in the oligomeric forms, and therefore were exclusively attributed to a quaternary structure change. Ligand binding as well as allosteric effectors and pH altered only the number of the T-contacted Tyr and Trp residues without varying the two contact states themselves. A new method to semiquantitatively evaluate the amount of T-contacted Tyr and Trp residues in a given liganded form is here proposed, and with it a quaternary structure was determined for various symmetrically half-liganded forms obtained with ligand-hybrid, metal-hybrid, and valency-hybrid Hbs. It was found that ligand binding to the α or β subunits yielded different subunit contacts and that the contact changes of the Trp and Tyr residues were not always concerted. The contact changes at the α(1)-β(2) (α(2)-β(1)) interface are correlated with the proximal strain exerted on the Fe-His(F8) bond, which is noted to be much larger in the α than β subunits in the α(2)β(2) tetramer.     

The genetic incorporation of a distance probe into proteins in Escherichia coli

The unnatural amino acid p-nitrophenylalanine (pNO2-Phe) was genetically introduced into proteins in Escherichia coli in response to the amber nonsense codon with high fidelity and efficiency by means of an evolved tRNA/aminoacyl-tRNA synthetase pair from Methanocuccus jannaschii. It was shown that pNO2-Phe efficiently quenches the intrinsic fluorescence of Trp in a distance-dependent manner in a model GCN4 basic region leucine zipper (bZIP) protein. Thus, the pNO2-Phe/Trp pair should be a useful biophysical probe of protein structure and function.     

Cis-trans photoisomerization of fluorescent-protein chromophores

Photochromic variants of fluorescent proteins are opening the way to a number of opportunities for high-sensitivity regioselective studies in the cellular environment and may even lead to applications in information and communication technology. Yet, the detailed photophysical processes at the basis of photoswitching have not been fully clarified. In this paper, we used synthetic FP chromophores to clarify the photophysical processes associated with the photochromic behavior. In particular, we investigated the spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein (GFP), Y66F GFP (BFPF), and Y66W GFP (CFP) upon irradiation in solutions of different polarities. We found that the cis-trans photoisomerization mechanism can be induced in all the chromophores. The structural assignments were carried out both by NMR measurements and DFT calculations. Remarkably, we determined for the first time the spectra of neutral trans isomers in different solvents. Finally, we calculated the photoconversion quantum yields by absorption measurements under continuous illumination at different times and by a nanosecond laser-flash photolysis method. Our results indicate that cis-trans photoisomerization is a general mechanism of FP chromophores whose efficiency is modulated by the detailed mutant-specific protein environment.     

Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair

We report the discovery of a simple system through which variant pyrrolysyl-tRNA synthetase/tRNA(CUA Pyl) pairs created in Escherichia coli can be used to expand the genetic code of Saccharomyces cerevisiae. In the process we have solved the key challenges of producing a functional tRNA(CUA Pyl) in yeast and discovered a pyrrolysyl-tRNA synthetase/tRNA(CUA Pyl) pair that is orthogonal in yeast. Using our approach we have incorporated an alkyne-containing amino acid for click chemistry, an important post-translationally modified amino acid and one of its analogs, a photocaged amino acid and a photo-cross-linking amino acid into proteins in yeast. Extensions of our approach will allow the growing list of useful amino acids that have been incorporated in E. coli with variant pyrrolysyl-tRNA synthetase/tRNA(CUA Pyl) pairs to be site-specifically incorporated into proteins in yeast.     

Tryptophan Photolysis Leads to a UVB-lnduced 66 kDa Photoproduct of Ribulose-1,5 Bisphosphate Carboxylase/Oxygenase (Rubisco) In Vitro and In Vivo

Abstract— Proteins are vulnerable to environmental UVB (290-320 nm) because aromatic amino acids, particularly Trp, absorb in this spectral region. We have shown previously that UVB impacts on ribulose-l,5-bisphosphate carboxylase/oxygenase (Rubisco), resulting in the formation of a 66 kDa photoproduct in vivo (Wilson et al, Plant Physiol. 109,221–229, 1995). To determine if Trp photolysis is involved in the production of this specific protein photoproduct, the effects of UVB on a homogeneous preparation of Rubisco were examined. A UVB photoproduct of 66 kDa, identical to the in vivo product, was formed in vitro. The 66 kDa product was shown by immunological methods to be a cross-link between a large subunit (53 kDa) and a small subunit (14 kDa). Time-resolved Trp fluorescence was used to demonstrate that a Trp fluorescence signal is lost with kinetics that mirror the rate of formation of the 66 kDa photoproduct, indicating that a Trp photolysis step is involved in the mechanism of photoproduct formation. The relative rates of both Trp photolysis and 66 kDa photoproduct formation did not change with Rubisco concentration, consistent with a monomolecular reaction that would occur between sub-units within a Rubisco holoenzyme complex. Finally, formation of the 66 kDa photoproduct was found to be pH dependent.     

Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae

Using a novel genetic selection, we have identified a series of mutants of the E. coli tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with p-(propargyloxy)phenylalanine and p-azidophenylalanine in yeast. These evolved tRNA-synthetase pairs can be used to site-specifically label proteins with functional groups orthogonal to normal biological chemistries. As an example, we have shown that proteins containing these amino acids can be efficiently bioconjugated with small organic molecules by a [3 + 2] cycloaddition reaction that is mild enough for the manipulation of biological samples.     

Molecular interaction in binary surfactant mixtures containing alkyl polyglycoside

Surface tensions were measured for several binary mixtures of a multidegree polymerized alkyl polyglycoside, C12G1.46' with different types of surfactants in 0.1 M NaCl at 25 degrees C. Based on regular solution theory, using a dimensional crystal model and a phase separation model, the molecule exchange energy in mixed monolayer formation (epsilon) and mixed micellization (epsilon(m)) were determined. Surfactants used in the mixtures with C12G1.46 in this study are C12E3S (trioxyethylenated dodecyl sulfonate), C12TAC (dodecyl trimethylammonium chloride), BE-6 (hexaoxyethylenated trisiloxane surfactant), and TMN-6 (hexaoxyethylenated-2,6,8-trimethylnonanol). The mixtures show exchange energy in mixed monolayer formation (epsilon) and mixed micellization (epsilon(m)) ranging from -660 to -1410 J/mol, indicating a decrease in surface energy upon mixing. The decreases in surface energy are in the order C12G1.46/C12E3S > C12G1.46/C12TAC, C12G1.46/C12TAC > C12G2/C12TAC and C12G1.46/BE-6 > C12G1.46/TMN-6. The ability of the mixed monolayer formation relative to the mixed micelle formation of the same binary mixture, measured by the (epsilon-epsilon(m)) values, is in the order C12G1.46/BE-6 > C12G1.46/TMN-6 > C12G1.46/C12E3S-->0 > C12G1.46/C12TAC.     

Electrosynthesis and electrochromic properties of free‐standing copolymer based on oligo(oxyethylene) cross‐linked 2,2’‐bithiophene and 3,4‐ethylenedioxythiophene

Oligo(oxyethylene) chains cross‐linked 2,2’‐bithiophene (BT‐E5‐BT) has been synthesized successfully. A free‐standing copolymer film based on BT‐E5‐BT and 3,4‐ethylenedioxythiophene (P(BT‐E5‐BT‐co‐EDOT)) has been synthesized by electrochemical polymerization. The electrical conductivity of P(BT‐E5‐BT‐co‐EDOT) copolymer (16 S m^?1) has improved by four orders of magnitude compared to the homopolymer of BT‐E5‐BT (P(BT‐E5‐BT), 5 × 10^?3 S m^?1) at room temperature. Both homopolymer and copolymer films exhibit well‐defined redox and satisfied coloration efficiency. Spectroelectrochemistry studies indicate that the P(BT‐E5‐BT‐co‐EDOT) has a lower band gap in the range of 1.83–1.90 eV and shows more plentiful electrochromic colours (green, blue, purple and salmon pink) compared with the homopolymer P(BT‐E5‐BT). The Copolymer P(BT‐E5‐BT‐co‐EDOT) shows the moderate optical contrast (26% of 480 nm) and coloration efficiency (205.41 cm^?1 C^?2). The copolymer method provides a novel way to fabricate a free‐standing organic electrochromic device. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 1583–1592     

Synthesis and evaluation of 1-deoxy-D-xylulose 5-phosphate analogues as chelation-based inhibitors of methylerythritol phosphate synthase

[structures: see text] A series of 1-deoxy-D-xylulose 5-phosphate (DXP) analogues were synthesized and evaluated as inhibitors of E. coli methylerythritol phosphate (MEP) synthase. In analogues 1-4, the methyl group in DXP was replaced by hydroxyl, hydroxylamino, methoxy, and amino moieties, respectively. In analogues 5 and 6, the acetyl moiety in DXP was replaced by hydroxymethyl and aminomethyl groups. These compounds were designed to coordinate to the active site divalent metal in MEP synthase. The carboxylate (1), methyl ester (3), amide (4), and alcohol (5) analogues were inhibitors with IC50's ranging from 0.25 to 1.0 mM. The hydroxamic acid (2) and amino (6) analogues did not inhibit the enzyme.     

A general approach for the generation of orthogonal tRNAs

BACKGROUND: The addition of new amino acids to the genetic code of Escherichia coli requires an orthogonal suppressor tRNA that is uniquely acylated with a desired unnatural amino acid by an orthogonal aminoacyl-tRNA synthetase. A tRNA(Tyr)(CUA)-tyrosyl-tRNA synthetase pair imported from Methanococcus jannaschii can be used to generate such a pair. In vivo selections have been developed for selecting mutant suppressor tRNAs with enhanced orthogonality, which can be used to site-specifically incorporate unnatural amino acids into proteins in E. coli. RESULTS: A library of amber suppressor tRNAs derived from M. jannaschii tRNA(Tyr) was generated. tRNA(Tyr)(CUA)s that are substrates for endogenous E. coli aminoacyl-tRNA synthetases were deleted from the pool by a negative selection based on suppression of amber nonsense mutations in the barnase gene. The remaining tRNA(Tyr)(CUA)s were then selected for their ability to suppress amber nonsense codons in the beta-lactamase gene in the presence of the cognate M. jannaschii tyrosyl-tRNA synthetase (TyrRS). Four mutant suppressor tRNAs were selected that are poorer substrates for E. coli synthetases than M. jannaschii tRNA(Tyr)(CUA), but still can be charged efficiently by M. jannaschii TyrRS. CONCLUSIONS: The mutant suppressor tRNA(Tyr)(CUA) together with the M. jannaschii TyrRS is an excellent orthogonal tRNA-synthetase pair for the in vivo incorporation of unnatural amino acids into proteins. This general approach may be expanded to generate additional orthogonal tRNA-synthetase pairs as well as probe the interactions between tRNAs and their cognate synthetases.     

Transformation of alpha-tocopherol (vitamin E) and related chromanol model compounds into their phenoxonium ions by chemical oxidation with the nitrosonium cation

[reaction: see text] Alpha-tocopherol (alpha-TOH), the main oil component making up vitamin E, and its nonnatural solid 6-hydroxy-2,2,5,7,8-pentamethylchroman and 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid structurally related analogues were oxidized quantitatively with 2 mol equiv of NO+ SbF6(-) in CH3CN at 233 K to form phenoxonium cations (alpha-TO+ SbF6(-)) in a chemically reversible two-electron/one-proton process. Solution-phase infrared spectroscopy, 1H and 13C NMR spectroscopy, and corresponding theoretical calculations of the spectroscopic data using density-based and wave-function-based models support the identity of the remarkably stable phenoxonium cations. The presence of an oxygen atom in the para position to the hydroxyl group and the chromanol ring structure appear to be important factors in stabilization of the phenoxonium ions, which raises the interesting possibility that the cations play a crucial role in the mode of action of vitamin E in biological systems. Although the phenoxonium cations are reactive toward nucleophiles such as water, they may be moderately stable in the hydrophobic (lipophilic) environment where vitamin E is known to occur naturally.     

Theory of laser enhancement of ultracold reactions: the fermion-boson population transfer by adiabatic passage of 6Li+6Li7Li(Tr=1 mK)-->6Li6Li+7Li(Tp=1 mK)

We present a new theory of population transfer by adiabatic passage. This theory relates laser catalysis to adiabatic passage, enhancing chemical reactions with the freedom to choose the translational energies of the reactants and products separately. The process, A+BC<-->(Planck's over omega(p) )ABC*(v)<-->(Planck's over omega(s))AB+C, involves two laser fields that are slowly varying so the process is adiabatic, and sufficiently intense so the population of the intermediate bound complex (ABC) is minimized. We apply this theory to the collinear exchange reaction (6)Li+(7)Li(2)(T(r))<-->(Planck's over omega(p))((6)Li(7)Li(7)Li)*<-->(variant Planck's over 2piomega(s) ) (6)Li(7)Li(T(p))+(7)Li. We show that at translational energies T(p)=T(r)=1 mK with a narrow energy bandwidth of delta(E)=0.01 mK, we can obtain nearly total (> or =98%) population transfer from the reactant to the product states. This can be done with a pump laser and a Stokes laser in an "intuitive" sequence (t(p)相似文献   

New organoselenium compounds active against pathogenic bacteria, fungi and viruses

Different N-substituted benzisoselenazol-3(2H)-ones, analogues of ebselen were designed as new antiviral and antimicrobial agents. We report their synthesis, chemical properties as well as study on biological activity against broad spectrum of pathogenic microorganisms (Staphylococcus aureus, Staphylococcus simulans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Candida albicans, Aspergillus niger) and viruses (herpes simplex virus type 1 (HSV-1), encephalomyocarditis virus (EMCV), vesicular stomatitis virus (VSV)), in vitro. Most of them exhibited high activity against viruses (HSV-1, EMCV) and gram-positive bacteria strains (S. aureus, S. simulans), while their activity against gram-negative bacteria strains (E. coli, P. aeruginosa, K. pneumoniae) was substantially lower. Some of tested compounds were active against yeast C. albicans and filamentous fungus A. niger.     

Molecular orbital calculations of ring opening of the isoelectronic cyclopropylcarbinyl radical, cyclopropoxy radical, and cyclopropylaminium radical cation series of radical clocks

Detailed molecular orbital calculations were directed to the cyclopropylcarbinyl radical (1), the cyclopropoxy radical (2), and the cyclopropylaminium radical cation (3) as well as their ring-opened products. Since a considerable amount of data are published about cyclopropylcarbinyl radicals, calculations were made for this species and related ring-opened products as a reference for 2 and 3 and their reactions. Radicals 1-3 have practical utility as "radical clocks" that can be used to time other radical reactions. Radical 3 is of further interest in photoelectron-transfer processes where the back-electron-transfer process may be suppressed by rapid ring opening. Calculations have been carried out at the UHF/6-31G*, MP4//MP2/6-31G*, DFT B3LYP/6-31G*, and CCSD(T)/cc-pVTZ//QCISD/cc-pVDZ levels. Energies are corrected to 298 K, and the barriers between species are reported in terms of Arrhenius E(a) and log A values along with differences in enthalpies, free energies, and entropies. The CCSD(T)-calculated energy barrier for ring opening of 1 is E(a) = 9.70, DeltaG* = 8.49 kcal/mol, which compares favorably to the previously calculated value of E(a) = 9.53 kcal/mol by the G2 method, but is higher than an experimental value of 7.05 kcal/mol. Our CCSD(T)-calculated E(a) value is also higher by 1.8 kcal/mol than a previously reported CBS-RAD//B3LYP/6-31G* calculation. The cyclopropoxy radical has a very small barrier to ring opening (CCSD(T), E(a) = 0.64 kcal/mol) and should be a very sensitive time clock. Of the three series studied, the cyclopropylaminium radical cation is most complex. In agreement with experimental data, bisected cyclopropylaminium radical cation is not found, but instead a ring-opened species is found. A perpendicular cyclopropylaminium radical cation (4) was found as a transition-state structure. Rotation of the 2p orbital in 4 to the bisected array results in ring opening. The minimum onset energy of photoionization of cyclopropylamine was calculated to be 201.5 kcal/mol (CCSD(T)) compared to experimental values of between about 201 and 204 kcal/mol. Calculations were made on the closely related cyclopropylcarbinyl and bicyclobutonium cations. Stabilization of the bisected cyclopropylcarbinyl conformer relative to the perpendicular species is much greater for the cations (29.1 kcal/ mol, QCISD) compared to the radicals (3.10 kcal/mol, QCISD). A search was made for analogues to the bicyclobutonium cation in the radical series 1 and 2 and the radical cation series 3. No comparable species were found. A rationale was made for some conflicting calculations involving the cyclopropylcarbinyl and bicyclobutonium cations. The order of stability of the cyclopropyl-X radicals was calculated to be X = CH2 > X = O > X = NH2+, where the latter species has no barrier for ring opening. The relative rate of ring opening for cyclopropyl-X radicals X = CH2 to X = O was calculated to be 3.1 x 10(6) s(-1) at 298 K (QCISD).     

Inhibitor scaffolds as new allele specific kinase substrates

The elucidation of protein kinase signaling networks is challenging due to the large size of the protein kinase superfamily (>500 human kinases). Here we describe a new class of orthogonal triphosphate substrate analogues for the direct labeling of analogue-specific kinase protein targets. These analogues were constructed as derivatives of the Src family kinase inhibitor PP1 and were designed based on the crystal structures of PP1 bound to HCK and N(6)-(benzyl)-ADP bound to c-Src (T338G). 3-Benzylpyrazolopyrimidine triphosphate (3-benzyl-PPTP) proved to be a substrate for a mutant of the MAP kinase p38 (p38-T106G/A157L/L167A). 3-Benzyl-PPTP was preferred by v-Src (T338G) (k(cat)/K(M) = 3.2 x 10(6) min(-)(1) M(-)(1)) over ATP or the previously described ATP analogue, N(6) (benzyl) ATP. For the kinase CDK2 (F80G)/cyclin E, 3-benzyl-PPTP demonstrated catalytic efficiency (k(cat)/K(M) = 2.6 x 10(4) min(-)(1) M(-)(1)) comparable to ATP (k(cat)/K(M) = 5.0 x 10(4) min(-)(1) M(-)(1)) largely due to a significantly better K(M) (6.4 microM vs 530 microM). In kinase protein substrate labeling experiments both 3-benzyl-PPTP and 3-phenyl-PPTP prove to be over 4 times more orthogonal than N(6)-(benzyl)-ATP with respect to the wild-type kinases found in murine spleenocyte cell lysates. These experiments also demonstrate that [gamma-(32)P]-3-benzyl-PPTP is an excellent phosphodonor for labeling the direct protein substrates of CDK2 (F80G)/E in murine spleenocyte cell lysates, even while competing with cellular levels (4 mM) of unlabeled ATP. The fact that this new more highly orthogonal nucleotide is accepted by three widely divergent kinases studied here suggests that it is likely to be generalizable across the entire kinase superfamily.