Multidimensional strategy for sensitive phosphoproteomics incorporating protein prefractionation combined with SIMAC, HILIC, and TiO(2) chromatography applied to proximal EGF signaling

Comprehensive enrichment and fractionation is essential to obtain a broad coverage of the phosphoproteome. This inevitably leads to sample loss, and thus, phosphoproteomics studies are usually only performed on highly abundant samples. Here, we present a comprehensive phosphoproteomics strategy applied to 400 μg of protein from EGF-stimulated HeLa cells. The proteins are separated into membrane and cytoplasmic fractions using sodium carbonate combined with ultracentrifugation. The phosphopeptides were separated into monophosphorylated and multiphosphorylated pools using sequential elution from IMAC (SIMAC) followed by hydrophilic interaction liquid chromatography of the mono- and nonphosphorylated peptides and subsequent titanium dioxide chromatography of the HILIC fractions. This strategy facilitated the identification of >4700 unique phosphopeptides, while 636 phosphosites were changing following short-term EGF stimulation, many of which were not previously known to be involved in EGFR signaling. We further compared three different data processing programs and found large differences in their peptide identification rates due to different implementations of recalibration and filtering. Manually validating a subset of low-scoring peptides exclusively identified using the MaxQuant software revealed a large percentage of false positive identifications. This indicates that, despite having highly accurate precursor mass determination, peptides with low fragment ion scores should not automatically be reported in phosphoproteomics studies.     

SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides

The complete analysis of phosphoproteomes has been hampered by the lack of methods for efficient purification, detection, and characterization of phosphorylated peptides from complex biological samples. Despite several strategies for affinity enrichment of phosphorylated peptides prior to mass spectrometric analysis, such as immobilized metal affinity chromatography or titanium dioxide, the coverage of the phosphoproteome of a given sample is limited. Here we report a simple and rapid strategy, SIMAC (sequential elution from IMAC), for sequential separation of monophosphorylated peptides and multiply phosphorylated peptides from highly complex biological samples. This allows individual analysis of the two pools of phosphorylated peptides using mass spectrometric parameters differentially optimized for their unique properties. We compared the phosphoproteome identified from 120 mug of human mesenchymal stem cells using SIMAC and an optimized titanium dioxide chromatographic method. More than double the total number of identified phosphorylation sites was obtained with SIMAC, primarily from a 3-fold increase in recovery of multiply phosphorylated peptides.     

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster

Reversible protein phosphorylation ranks among the most important post-translational modifications, and elucidation of phosphorylation sites is essential to understand the regulation of key cellular processes such as signal transduction. Enrichment of phosphorylated peptides is a prerequisite for successful analysis due to their low stoichiometry, heterogeneity, and low abundance. Enrichment is often performed manually, which is inherently labor-intensive and a major hindrance in large-scale analyses. Automation of the enrichment method would vastly improve reproducibility and thereby facilitate 'high-throughput' phosphoproteomics research. Here, we describe a robust and automated online TiO 2-based two-dimensional chromatographic approach to selectively enrich phosphorylated peptides from digests of complete cellular lysates. We demonstrate method enhancement for both adsorption and desorption of phosphorylated peptides resulting in lower limits of detection. Phosphorylated peptides from a mere 500 attomole tryptic digest of a protein mixture were easily detected. With the combination of strong cation exchange chromatography with the online TiO 2 enrichment, 2152 phosphopeptides were enriched from 250 microg of protein originating for the cell lysate of Drosophila melanogaster S2 cells. This is a 4-fold improvement when compared to an enrichment strategy based solely on strong cation exchange/LC-MS. Phosphopeptide enrichment methods are intrinsically biased against relatively basic phosphopeptides. Analysis of the p I distributions of the enriched/detected phosphopeptides showed that the p I profile resembles that of a total Drosophila protein digest, revealing that the current described online procedure does not discriminate against either more acidic or basic phosphopeptides. However, careful comparison of our new and existing phosphopeptide enrichment techniques also reveal that, like many enrichment techniques, we are still far from comprehensive phosphoproteomics analyses, and we describe several factors that still require to be addressed. Still, as the online approach allows the complementary measurements of phosphopeptides and their nonphosphorylated counterparts in subsequent analyses, this method is well-suited for automated quantitative phosphoproteomics.     

Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches

Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for mapping of phosphosites. However, because of sample complexity, fractionation of phosphopeptides prior to MS analysis is a crucial step. In the current study, we compare the chromatographic strategies electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), hydrophilic interaction liquid chromatography (HILIC), and strong cation exchange chromatography (SCX) for their fractionation behavior of phosphopeptides. In addition, we investigate the use of repetitive TiO(2)-based enrichment steps for a maximum identification of phosphopeptides. On the basis of our results, SCX yields the highest number of identified phosphopeptides, whereas ERLIC is optimal for the identification of multiphosphorylated peptides. Consecutive incubations of fractions and flow-through by TiO(2) beads enrich qualitatively different sets of phosphopeptides, increasing the number of identified phosphopeptides per analysis.     

MALS: an efficient strategy for multiple site-directed mutagenesis employing a combination of DNA amplification, ligation and suppression PCR

Background

The cattle ticks, Boophilus spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant B. microplus Bm86 protective antigen has been shown to protect cattle against tick infestations. Recently, the gene coding for B. annulatus Bm86 ortholog, Ba86, was cloned and the recombinant protein was secreted and purified from the yeast Pichia pastoris.

Results

Recombinant Ba86 (Israel strain) was used to immunize cattle to test its efficacy for the control of B. annulatus (Mercedes, Texas, USA strain) and B. microplus (Susceptible, Mexico strain) infestations. Bm86 (Gavac and Mozambique strain) and adjuvant/saline were used as positive and negative controls, respectively. Vaccination with Ba86 reduced tick infestations (71% and 40%), weight (8% and 15%), oviposition (22% and 5%) and egg fertility (25% and 50%) for B. annulatus and B. microplus, respectively. The efficacy of both Ba86 and Bm86 was higher for B. annulatus than for B. microplus. The efficacy of Ba86 was higher for B. annulatus (83.0%) than for B. microplus (71.5%). The efficacy of Bm86 (Gavac; 85.2%) but not Bm86 (Mozambique strain; 70.4%) was higher than that of Ba86 (71.5%) on B. microplus. However, the efficacy of Bm86 (both Gavac and Mozambique strain; 99.6%) was higher than that of Ba86 (83.0%) on B. annulatus.

Conclusion

These experiments showed the efficacy of recombinant Ba86 for the control of B. annulatus and B. microplus infestations in cattle and suggested that physiological differences between B. microplus and B. annulatus and those encoded in the sequence of Bm86 orthologs may be responsible for the differences in susceptibility of these tick species to Bm86 vaccines.     

MALS: an efficient strategy for multiple site-directed mutagenesis employing a combination of DNA amplification, ligation and suppression PCR

Background  

Multiple approaches for the site-directed mutagenesis (SDM) have been developed. However, only several of them are designed for simultaneous introduction of multiple nucleotide alterations, and these are time consuming. In addition, many of the existing multiple SDM methods have technical limitations associated with type and number of mutations that can be introduced, or are technically demanding and require special chemical reagents.     

Deconica cokeriana (Agaricales,Strophariaceae), a new combination

Deconica cokeriana is proposed as a new combination based on morphological and molecular data. This species is fully described, discussed, and illustrated. Until now, D. cokeriana is only known from the eastern USA, specifically from Connecticut, Georgia, Ohio, and Tennessee.     

Measuring hydrogen peroxide reduction using a robust, inexpensive, and sensitive method

Here, we report an improved method to analyze antioxidant activity using the europium tetracycline assay developed by Duerkop and Wolfbeis (J Fluor 15(5):755–761, 2005). The europium tetracycline hydrogen peroxide reduction assay (EHRA) accurately measures antioxidant activity based on hydrogen peroxide scavenging. Several known antioxidant compounds were assessed with the EHRA and a stoichiometric relationship between the number of oxidant molecules trapped per molecule of antioxidant was identified. Various extracts of hops were also tested to validate this method for use with natural extracts; water extraction yielded the highest level of antioxidant activity. Hop leaves were shown to be a better source of antioxidants relative to the traditional hop cones. The data also indicate that the EHRA may serve to breach the hydrophilic/lipophilic gap in antioxidant screening as the europium tetracycline probe is effective in many solvents. The EHRA thus provides a robust and inexpensive measure of antioxidant activity.     

豆科长柄山蚂蝗属一新组合

Ohashi和Mill提出长柄山蚂蝗属的正确学名是Hylodesmum H.Ohashi&R.R.Mill,用以取代由来已久的属名Podocarpium（Benth.）Y.C.Yang&P.H.Huang。本文根据该属属名的变化,提出并确定澜沧长柄山蚂蝗的新组合名称为Hylodesmum lancangense（Y.Y.Qian X.Y.Zhu&H.Ohashi。     

Comparative properties of sensitive to GABAA-ergic ligands, Cl(-), HCO3(-)-activated Mg2+-ATPase from brain plasma membranes of fish and rats

Action of Cl(-) + HCO3(-) ions on Mg2+-ATPase from brain plasma membranes of fish and rats has been studied. Maximal effect of the anions on the Mg2+-ATPase activity is revealed in the presence of 10 mM Cl(-) and 3 mM HCO3(-) at physiological values of pH of incubation medium. The studied Cl(-), HCO3(-)-activated Mg2+-ATPases of both animal species, by their sensitivity to SH-reagents (5,5-dithiobis-nitrobenzoic acid, N-ethylmaleimide), oligomycin, and orthovanadate, are similar to transport ATPase of the P-type, but differ from them by molecular properties and by sensitivity to ligands of GABAA-receptors. It has been established that the sensitive to GABAA-ergic ligands, Cl(-), HCO3(-)-activated Mg2+-ATPase from brain of the both animal species is protein of molecular mass around 300 kDa and of Stocks' radius 5.4 nm. In fish the enzyme is composed of one major unit of molecular mass approximately 56 kDa, while in rats--of three subunits of molecular masses about 57, 53, and 45 kDa. A functional and structural coupling of the ATP-hydrolyzing areas of the studied enzyme to sites of binding of GABAA-receptor ligands is suggested.     

SARS-CoV-2 Omicron variant is highly sensitive to molnupiravir,nirmatrelvir,and the combination

Dear Editor, Since the first outbreak in late 2019,the RNA genome of SARS-CoV-2 has been undergoing constant evolution.This is largely attributed to the viral p...     

Spectroscopic and reactivity comparison of pentacyanonitrosylruthenate(2-) with pentacyanonitrosylferrate(2-), nitroprusside

Lithium penta(cyano-¹³C)nitrosylruthenate (2-), Li₂[Ru(¹³CN)₅NO], in which the anion is the ruthenium analogue of the nitroprusside ion, has been synthesized at 90% isotopic enrichment, and characterized spectroscopically. Despite the very high level of ¹³C enrichment, no two-bond coupling ²J(¹³C_ax-Ru¹³C_eq) was detected in the high-frequency ¹³C NMR spectrum of Li₂[Ru(¹³CN)₅NO], nor was any such coupling observed in Li₄[Ru(¹³CN)₅(¹⁵NO₂)] although both two-bond couplings to ¹⁵N, ²J(¹³C_ax-Ru¹⁵NO₂) and ²J(¹³C_eqRu¹⁵N) were observed. Li₂[Ru(¹³CN)₅(¹⁴NO)] reacted with excess of Li[¹⁵NO₂] to yield Li₄[Ru(¹³CN)₅(¹⁵NO₂)] only: no Li₂[Ru(¹³CN)₅(¹⁵NO)] was observed. Li₄[Ru(¹³CN)₅(¹⁴NO₂)] however showed no exchange with Li[¹⁵NO₂]. While [Ru(CN)₅NO]²⁻ reacted with both OH⁻ and SH⁻ in reactions similar to those of [Fe(CN)₅NO]²⁻, no reactions were detected between [Ru(CN)₅NO]²⁻ and piperidine, [CH(CN)₂]⁻, [CH(COCH₃)₂]⁻, MeS⁻, or [S₂O₄]²⁻, all of which are known to react readily with [Fe(CN)₅NO]²⁻     

IMAC/TiO(2) enrich for peptide modifications other than phosphorylation: implications for chromatographic choice and database searching in phosphoproteomics

Protein regulation by reversible phosphorylation is fundamental in nature, and large-scale phosphoproteomic analyses are becoming routine in proteomics laboratories. These analyses utilise phosphopeptide separation and enrichment techniques linked to LC-MS/MS. Herein, we report that IMAC and TiO(2) also enrich for non-phosphorylated modified peptides such as acetylated, deamidated and carbamylated peptides. Urea and digestion conditions commonly used in phosphoproteomic workflows are the likely sources of the induced modifications (deamidation and carbamylation) and can easily modify phosphopeptides. Including these variable modifications in database searches increased the total number of identified phosphopeptides by 15%. We also show that strong cation exchange fractionation provides poor resolution of phosphopeptides and actually enriches these alternatively modified peptides. By switching to reverse-phase chromatography, we show a significant improvement in the number of identified phosphopeptides. We recommend that the users of phosphopeptide enrichment strategies avoid using urea as a denaturant and that careful consideration is given to chromatographic conditions and the types of variable modifications used in database searches. Thus, the capacity of IMAC and TiO(2) to enrich phosphopeptides bearing modifications other than phosphorylation is a previously unappreciated property of these chromatographies with practical implications for the field of phosphoproteomics.     

Enantioselective synthesis and absolute configuration of (-)-1-(benzofuran-2-yl)-2-propylaminopentane, ((-)-BPAP), a highly potent and selective catecholaminergic activity enhancer

Enantioselective synthesis and absolute configuration of (-)-1-(benzofuran-2-yl)-2-propylaminopentane ((-)-BPAP), which is a highly potent and selective catecholaminergic activity enhancer (CAE) substance, are described. The synthetic approach consists of the coupling reaction of benzofuran with (R)-N-tosyl-2-propylazirizine or (R)-N-methoxy-N-methylnorvaliamide, followed by appropriate modifications of the resulting coupling products. As the results, (-)-BPAP turned out to have the R configuration, which was finally confirmed by X-ray crystallographic analysis.     

Discovery of betrixaban (PRT054021), N-(5-chloropyridin-2-yl)-2-(4-(N,N-dimethylcarbamimidoyl)benzamido)-5-methoxybenzamide,a highly potent,selective, and orally efficacious factor Xa inhibitor

Systematic SAR studies of in vitro factor Xa inhibitory activity around compound 1 were performed by modifying each of the three phenyl rings. A class of highly potent, selective, efficacious and orally bioavailable direct factor Xa inhibitors was discovered. These compounds were screened in hERG binding assays to examine the effects of substitution groups on the hERG channel affinity. From the leading compounds, betrixaban (compound 11, PRT054021) has been selected as the clinical candidate for development.     

Structural analysis of the O-antigen side chain polysaccharides in the lipopolysaccharides of Klebsiella serotypes O2(2a), O2(2a,2b), and O2(2a,2c).

The lipopolysaccharide (LPS) of Klebsiella serotype O2 is antigenically heterogeneous; some strains express multiple antigenic factors. To study this heterogeneity, we determined the structure of the O-antigen polysaccharides in isolates belonging to serotypes O2(2a), O2(2a,2b), and O2(2a,2c), by using composition analysis, methylation analysis, and both 1H and 13C nuclear magnetic resonance spectroscopy. The repeating unit structure of the 2a polysaccharide was identified as the disaccharide [----3)-beta-D-Galf-(1----3)-alpha-D-Galp-(1----] and was identical to D-galactan I, one of two O polysaccharides present in the LPS of Klebsiella pneumoniae serotype O1 (C. Whitfield, J. C. Richards, M. B. Perry, B. R. Clarke, and L. L. MacLean, J. Bacteriol. 173:1420-1431, 1991). LPS from serotype O2(2a,2b) also contained D-galactan I as the only O polysaccharide, suggesting that the 2b antigen is not an O antigen. The LPS of serotype O2(2a,2c) contained a mixture of two structurally distinct O polysaccharides and provides a second example of this phenomenon in Klebsiella spp. One polymer was identical to D-galactan I, and the other polysaccharide, the 2c antigen, was a polymer with a disaccharide repeating unit structure, [----3)-beta-D-GlcpNAc-(1----5)-beta-D-Galf-(1----]. The 2c structure does not resemble previously reported O polysaccharides from Klebsiella spp. Periodate oxidation confirmed that D-galactan I and the 2c polysaccharide are distinct glycans, rather than representing domains within a single polysaccharide chain. Monoclonal antibodies against the 2c antigen indicated that only LPS molecules with the longest O-polysaccharide chains contained the 2c epitope.     

Antiviral effects of 2',5'oligoadenylates (2-5As), and related compounds

Dephosphorylated "core" of 2',5'-oligoadenylate (2-5A) dimer (A2'p5'A), exogenously added to nonpermeabilized FL cells, inhibited the multiplication of Sindbis virus and vesicular stomatitis virus (VSV). The compound was shown to inhibit viral protein synthesis. The addition of A2'p5'A at the early stage of viral replication was more effective than that at the late stage. In contrast with the core, phosphorylated 2-5A (p5'A2'p5'A and ppp5'A2'p5'A) and 2-5A analogs containing cordycepin (3'-deoxyadenosine) did not show such antiviral effects. The rate of uptake of [3H]ppp5'A 2'p5'A into acid-soluble and acid-insoluble fractions, especially into the acid-insoluble fraction, was faster than that of [3H]A2'p5'A. These results suggest that the difference of antiviral activity between A2'p5'A and ppp5'A2'p5'A does not result from the different rate of uptake by cells, but from the different rate of from acid-soluble to acid-insoluble fractions.     

Photocatalytic antimicrobial activity of thin surface films of TiO(2), CuO and TiO (2)/CuO dual layers on Escherichia coli and bacteriophage T4

TiO₂-coated surfaces are increasingly studied for their ability to inactivate microorganisms. The activity of glass coated with thin films of TiO₂, CuO and hybrid CuO/TiO₂ prepared by atmospheric Chemical Vapour Deposition (Ap-CVD) and TiO₂ prepared by a sol–gel process was investigated using the inactivation of bacteriophage T4 as a model for inactivation of viruses. The chemical oxidising activity was also determined by measuring stearic acid oxidation. The results showed that the rate of inactivation of bacteriophage T4 increased with increasing chemical oxidising activity with the maximum rate obtained on highly active sol–gel preparations. However, these were delicate and easily damaged unlike the Ap-CVD coatings. Inactivation rates were highest on CuO and CuO/TiO₂ which had the lowest chemical oxidising activities. The inactivation of T4 was higher than that of Escherichia coli on low activity surfaces. The combination of photocatalysis and toxicity of copper acted synergistically to inactivate bacteriophage T4 and retained some self-cleaning activity. The presence of phosphate ions slowed inactivation but NaCl had no effect. The results show that TiO₂/CuO coated surfaces are highly antiviral and may have applications in the food and healthcare industries.     

N-(6-Aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), a calmodulin antagonist,also inhibits phospholipid sensitive calcium-dependent protein kinase

N-(6-Aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), commonly regared as a calmodulin antagonist, inhibted phospholipid-sensitive Ca²⁺-dependent protein kinase and to a lesser extent cyclic GMP- and cyclic AMP-dependent protein kinases. Kinetic studies of the inhibition of the homogenous spleen phospholipid-sensitive Ca²⁺-dependent protein kinase indicated that W-7 inhibited the enzyme activity competitively with respect to phospholipid (K_i = 60 μM). N-(6-Aminohexyl)-1-naphthalenesulfonamide (W-5) was found to be musch less potent than W-7. The findings indicate that W-6 was able to inhibit a variety of protein kinases, in addition to those requiring calmodulin previously reported.