Identification of nitrated tyrosine residues of protein kinase G-Iα by mass spectrometry

The nitration of tyrosine to 3-nitrotyrosine is an oxidative modification of tyrosine by nitric oxide and is associated with many diseases, and targeting of protein kinase G (PKG)-I represents a potential therapeutic strategy for pulmonary hypertension and chronic pain. The direct assignment of tyrosine residues of PKG-I has remained to be made due to the low sensitivity of the current proteomic approach. In order to assign modified tyrosine residues of PKG-I, we nitrated purified PKG-Iα expressed in insect Sf9 cells by use of peroxynitrite in vitro and analyzed the trypsin-digested fragments by matrix-assisted laser desorption/ionization–time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Among the 21 tyrosine residues of PKG-Iα, 16 tyrosine residues were assigned in 13 fragments; and six tyrosine residues were nitrated, those at Y71, Y141, Y212, Y336, Y345, and Y567, in the peroxynitrite-treated sample. Single mutation of tyrosine residues at Y71, Y212, and Y336 to phenylalanine significantly reduced the nitration of PKG-Iα; and four mutations at Y71, Y141, Y212, and Y336 (Y4F mutant) reduced it additively. PKG-Iα activity was inhibited by peroxynitrite in a concentration-dependent manner from 30 μM to 1 mM, and this inhibition was attenuated in the Y4F mutant. These results demonstrated that PKG-Iα was nitrated at multiple tyrosine residues and that its activity was reduced by nitration of these residues.     

Allosteric regulation of protein kinase PKCζ by the N-terminal C1 domain and small compounds to the PIF-pocket

Protein kinases are key mediators of cellular signaling, and therefore, their activities are tightly controlled. AGC kinases are regulated by phosphorylation and by N- and C-terminal regions. Here, we studied the molecular mechanism of inhibition of atypical PKCζ and found that the inhibition by the N-terminal region cannot be explained by a simple pseudosubstrate inhibitory mechanism. Notably, we found that the C1 domain allosterically inhibits PKCζ activity and verified an allosteric communication between the PIF-pocket of atypical PKCs and the binding site of the C1 domain. Finally, we developed low-molecular-weight compounds that bind to the PIF-pocket and allosterically inhibit PKCζ activity. This work establishes a central role for the PIF-pocket on the regulation of PKCζ and allows us to envisage development of drugs targeting the PIF-pocket that can either activate or inhibit AGC kinases.     

Analysis of autophosphorylation sites in the recombinant catalytic subunit alpha of cAMP-dependent kinase by nano-UPLC–ESI–MS/MS

The catalytic subunit of recombinant wild-type cyclic adenosine monophosphate-dependent protein kinase A (PKA) has been analyzed by a combination of 1D gel electrophoresis, in-gel digestion by trypsin, chymotrypsin, or endoproteinase AspN, and nano-ultraperformance liquid chromatography–MS/MS. The MS/MS spectra were annotated by MASCOT and the annotations were manually controlled. Using Ga(III)-immobilized metal ion affinity chromatography (IMAC), in addition to the four established autophosphorylation sites of the catalytic subunit of recombinant PKA, pSer10, pSer139, pThr197, and pSer338, six new phosphorylated residues have been characterized–pSer14, pThr48, pSer53, pSer212, pSer259, and pSer325. The established phosphorylation sites all are part of a PKA consensus motif and were found to be almost completely modified. In contrast, the newly detected sites were only partially phosphorylated. For estimation of their degree of phosphorylation, a method based on signal intensity measurements was used. For this purpose, signal intensities of all phospho- and non-phosphopeptides containing a particular site were added for estimation of site-specific phosphorylation degrees. This addition was performed over all peptides observed in the different digestion experiments, including their different charge states. pThr48 and pSer259 are located within PKA consensus motifs and were observed to be phosphorylated at 20% and 24%, respectively. pSer14 and pSer53 are located within inverted PKA consensus motifs and were found to be phosphorylated around 10% and 15%, respectively. The sequence environments of pSer212 and pSer325 have no similarity to the PKA consensus motif at all and were observed to be phosphorylated at about 5% or lower. All newly observed phosphorylation sites are located at the surface of the native protein structure of the PKA catalytic subunit. The results add new information on the theme of site-specific (auto)phosphorylation by PKA.      

Generation of cytidine 5′-triphosphate using adenylate kinase

A membrane-enclosed enzyme reactor containing adenylate kinase (E.C. 2.7.4.3, rabbit muscle) and pyruvate kinase (E.C. 2.7.1.40) converts cytidine 5′-monophosphate (CMP) and phosphoenolpyruvate (PEP) to cytidine 5′-triphosphate (CTP) and pyruvate on a gram scale.     

Modification of β2 I by glutardialdehydeI by glutardialdehyde

Autoantibodies from patients with antiphospholipid syndrome (APS) recognize an epitope on β₂glycoprotein I (β₂GPI) only when native β₂GPI is adsorbed on surfaces composed of anionic phospholipids or oxidized polystyrene, β₂GPI was modified with the crosslinking agent, glutardialdehyde (GDA), which induced exposure of the anti-β₂GPI epitope at GDA: β₂GPI mol ratios in the range of 500–2000. A second crosslinking agent, dimethyl-suberimidate (DMS), did not expose the epitope, which may be a consequence of its having less tendency than GDA to form intermolecular links. SDS-PAGE experiments demonstrate that GDA does promote extensive intermolecular crosslinking of β₂GPI, and DMS does not. Formaldehyde also reacts with the lysine residues of β₂GPI, but does not expose the epitope. The circular dichroism spectra of native and modified β₂GPI confirm that GDA induces changes in conformation that are qualitatively different from those caused by formaldehyde. These data provide evidence that binding of lysine residues is not a sufficient condition for exposure of the autoepitope, and also support the likelihood that β₂GPI antibodies bind only to aggregates of the protein. Thus, by synthesizing an active holoantigen of β₂GPI, conditions were defined that are necessary for binding of human autoantibodies. The authors also suggest that treatment of phospholipid-binding proteins with chemical agents might provide a strategy to modify their structure and permit exposure of epitopes, resulting in synthetic antigens for therapeutic and diagnostic use.     

Enantiomer separation by CEC——Enantiomer separation by packed-capillary electrochromatography

Three chiral compounds were successfully separated in a short time with two enantiomer separation models on packed-capillary electrochromatography (CEC). (i) 75 μm I.D. capillaries were packed with 5 μm β-cyclodextrin (β-CD) chiral stationary phase (CSP). Effects of voltage, pH and concentration of organic modifier on electroosmotic flow (EOF) and chiral separations were investigated systematically. Enantiomers of a neutral compound (benzoin) and a neutral drug (mephenytoin) were separated within a short time with high efficiency. Efficiency of 32 000 theoretical plates per meter and resolution (R_s) of 1.42 were achieved for enantiomers of benzoin using a βCD packed column with 6.2 cm packed length. Efficiency of 45 000 theoretical plates per meter and R_s of 3.40 were obtained for enantiomers of mephenytoin. Especially, the enantiomer separation of mephenytion was performed in just 3.4 min with R_s of 2.60. (ⅱ) 75 μm I.D. capillary was packed with octadecylsilica particles (ODS). Chiral separat     

Molecular characterization of protein kinase C delta (PKCδ)-Smac interactions

Background

Protein kinase C δ (PKCδ) is known to be an important regulator of apoptosis, having mainly pro- but also anti-apoptotic effects depending on context. In a previous study, we found that PKCδ interacts with the pro-apoptotic protein Smac. Smac facilitates apoptosis by suppressing inhibitor of apoptosis proteins (IAPs). We previously established that the PKCδ-Smac complex dissociates during induction of apoptosis indicating a functional importance. Because the knowledge on the molecular determinants of the interaction is limited, we aimed at characterizing the interactions between PKCδ and Smac.

Results

We found that PKCδ binds directly to Smac through its regulatory domain. The interaction is enhanced by the PKC activator TPA and seems to be independent of PKCδ catalytic activity since the PKC kinase inhibitor GF109203X did not inhibit the interaction. In addition, we found that C1 and C2 domains from several PKC isoforms have Smac-binding capacity.

Conclusions

Our data demonstrate that the Smac-PKCδ interaction is direct and that it is facilitated by an open conformation of PKCδ. The binding is mediated via the PKCδ regulatory domain and both the C1 and C2 domains have Smac-binding capacity. With this study we thereby provide molecular information on an interaction between two apoptosis-regulating proteins.

     

CO2 activation by metal−ligand-cooperation mediated by iridium pincer complexes

Abstract

Herein we report the reversible activation of CO₂ by the dearomatized complex [(^tBuPNP*)Ir(COE)] (1) and by the aromatized complex [(^tBuPNP)Ir(C₆H₅)] (2) via metal-ligand cooperation (MLC) (^tBuPN = 2,6-bis-(di-tert-butylphosphinomethyl)pyridine; ^tBuPNP* = deprotonated PNP; COE = cyclooctadiene). The [1,3]-addition of CO₂ to 1 and 2 is reversible at ambient temperature. While the dearomatized complex 1 reacts readily at ambient temperature with CO₂ in THF or benzene, complex 2 reacts with CO₂ upon heating in benzene at 80 °C or at ambient temperature in THF. The novel aromatized complex [(^tBuPNP)IrCl] (10) does not react with CO₂. Based on the reactivity patterns of 1, 2, and 10 with CO₂, we suggest that CO₂ activation via MLC takes place only via the dearomatized species, and that in the case of 2 THF plays a role as a polar solvent in facilitating formation of the dearomatized hydrido phenyl complex intermediate (complex II).     

β-secretase 1 inhibitory activity and AMP-activated protein kinase activation of Callyspongia samarensis extracts

Abstract

The methanolic extract of Callyspongia samarensis (MCS) significantly inhibited β-secretase 1 (IC₅₀ 99.82?µg/mL) in a dose-dependent manner and demonstrated a noncompetitive type of inhibition. Furthermore, it exhibited the highest AMPK activation (EC₅₀ 14.47?μg/mL) as compared with the standard, Aspirin (EC₅₀ >100?μg/mL). HPLC/ESI-MS analysis of MCS extract revealed 15 peaks, in which nine peaks demonstrated similar fragmentation pattern with the known compounds in literature and in database library: 5-aminopentanoic acid (1), 4-aminobutanoic acid (3), Luotonin A (4), (E)-3-(1H-imidazol-5-yl) prop-2-enoic acid (8), Galactosphingosine (10), D-sphingosine (11), 5,7,4′-trihydroxy-3′,5′-dimethoxyflavone (12), hydroxydihydrovolide (13), and 3,5-dibromo-4-methoxyphenylpyruvic acid (14); and 6 peaks are not identified (2, 5–7, 9, and 15). Acute oral toxicity test of MCS extract revealed that it is nontoxic, with an LD₅₀ of >2000?mg/kg. Assessment of BBB permeability of MCS extract showed that compound 15 was able to cross the BBB making it a suitable candidate for developing CNS drugs.     

Synthesis and CDK2 kinase inhibitory activity of 7/7′-azaindirubin derivatives

<正>A series of novel 7'-azaindirubin(1a-g) and 7-azaindirubin(2a,2c,2e and 2f) derivatives were designed and synthesized.Their structures were characterized by ~1H NMR and MS spectroscopy as well as by elemental analysis.Their inhibitory properties against CDK2/cylinA were evaluated in vitro.In contrast to indirubin,some of the described azaindirubins emerged as potent inhibitors of CDK2/cylinA and compound 2b had more potent activity.Biological tests also showed that nitrogen atom at 7-position of azaindirubin was more beneficial to enhance the kinase inhibitory activity.     

Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?

An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.     

Asymmetric Syntheses Aided by Biocatalysts

This article summarizes the achievements of the authors‘ group in the area of biocatalyst-catalyzed organic reactions in recent 10 years. A strain of Geotrichum sp. obtained by screeninu is capable of stereoselectlvely reducing a number of carbonyl compounds. In many cases, the stermghemistry is complementary with that obtained by baker‘ s yeast. Therefore, this microorganism provides a useful pathway to the preparation of alcohol eompounds with specific configurations. On the other hand, a nmmber of plant sourees have been screened for oxynitrilases and the hydrocyanation reactions of various arylcarboxalde-hydes have been investigated.A“micro-aqueous reaction system“ was invented,by which a serles of novel optically active cyanohydrins were prepared.On this hasis,a high through-put comtimasous reaction system has been designed.This paper also deseribes examples of the syntheses of bio-active compounds by using the optieally active compounds obtained from the above mentioned catalytic reactions as precursors.     

Renewable β-Myrcene Polymerization Initiated by Lutetium Alkyl Complexes Ligated by Imidophosphonamido Ligand

β-Imidophosphonamido ligated lutetium alkyl complex(NPNDipp)Lu(CH2Si Me3)2(THF)(NPNDipp = Ph2P(NC6H3iPr2-2,6)2) with the activation of AliBu3 and [Ph3C][B(C6F5)4] exhibited high catalytic activity, medium syndio-(rr = 66%) but remarkably high 3,4-regioselectivity for the polymerization of β-myrcene(MY). In sharp contrast, high isotactic 3,4-polymyrcene(PMY)(mm = 95%) was obtained by the precursor(NPNEt)Lu(CH2Si Me3)2(THF)(NPNEt = PPh2(NC6H3iPr2-2,6)(NC6H4-Et-2)) with less bulky substituents on the N-aryl ring.     

Molecular-Sieving Membrane by Partitioning the Channels in Ultrafiltration Membrane by In Situ Polymerization

Commercial ultrafiltration membranes have proliferated globally for water treatment. However, their pore sizes are too large to sieve gases. Conjugated microporous polymers (CMPs) feature well-developed microporosity yet are difficult to be fabricated into membranes. Herein, we report a strategy to prepare molecular-sieving membranes by partitioning the mesoscopic channels in water ultrafiltration membrane (PSU) into ultra-micropores by space-confined polymerization of multi-functionalized rigid building units. Nine CMP@PSU membranes were obtained, and their separation performance for H₂/CO₂, H₂/N₂, and H₂/CH₄ pairs surpass the Robeson upper bound and rival against the best of those reported membranes. Furthermore, highly crosslinked skeletons inside the channels result in the structural robustness and transfer into the excellent aging resistance of the CMP@PSU. This strategy may shed light on the design and fabrication of high-performance polymeric gas separation membranes.     

"Pure by NMR"?

Integration of a (13)C-(1)H satellite peak of a given (12)C-(1)H parent resonance within a quantitative (1)H NMR spectrum and comparison to the minor component represents a simple protocol for the accurate determination of diastereoisomeric ratios of up to 1000:1 (i.e., 99.8% de).     

Can crude oils be distinguished by different component distribution obtained by laser desorption ionization mass spectrometry and evaluated by chemometrics?

Fourteen different crude oil samples were analyzed as collected by mass spectrometry. For two of them the results obtained by means of different techniques, i.e. electrospray ionization, atmospheric pressure chemical ionization, laser desorption/ionization, were compared. The latter technique leads to the best results: even if unable to give specific information on heteroatom-containing components, it allows a general view to be obtained of the panorama of the oil composition in terms of molecular weight distribution. The statistical evaluation of the mass spectrometry data by multivariate techniques, such as cluster analysis (Average Linkage) and correspondence analysis, allows evidence for the differences and similarities among the crude oils under study.     

Knoevenagel Condensation Catalysed by Alumina

在Ａｌ２Ｏ３催化下活泼亚甲基化合物和羰基化合物进行克脑文格尔缩合反应，在温和的反应条件下得到较高收率的产物。将超声波辐射应用于该缩合反应使反应速度明显提高。     

Glucose biosensor enhanced by nanoparticles

Glucose biosensors have been formed with glucose oxidase (GOD) immobilized in composite immobilization membrane matrix, which is composed of hydrophobic gold, or hydro-philic gold, or hydrophobic silica nanoparticles, or the combination of gold and silica nanoparticles, and polyvinyl butyral (PVB) by a sol-gel method. The experiments show that nanoparticles can significantly enhance the catalytic activity of the immobilization enzyme. The current response can be increased from tens of nanoamperometer (nA) to thousands of nanoamperometer to the same glucose concentration, and the electrodes respond very quickly, to about 1 min. The function of nanoparticles effect on immobilization enzyme has been discussed.