Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

Despite significant efforts in the past decade toward complete mapping of the human proteome, 3564 proteins (neXtProt, 09-2014) are still "missing proteins". Over one-third of these missing proteins are annotated as membrane proteins, owing to their relatively challenging accessibility with standard shotgun proteomics. Using nonsmall cell lung cancer (NSCLC) as a model study, we aim to mine missing proteins from disease-associated membrane proteome, which may be still largely under-represented. To increase identification coverage, we employed Hp-RP StageTip prefractionation of membrane-enriched samples from 11 NSCLC cell lines. Analysis of membrane samples from 20 pairs of tumor and adjacent normal lung tissue was incorporated to include physiologically expressed membrane proteins. Using multiple search engines (X!Tandem, Comet, and Mascot) and stringent evaluation of FDR (MAYU and PeptideShaker), we identified 7702 proteins (66% membrane proteins) and 178 missing proteins (74 membrane proteins) with PSM-, peptide-, and protein-level FDR of 1%. Through multiple reaction monitoring using synthetic peptides, we provided additional evidence of eight missing proteins including seven with transmembrane helix domains. This study demonstrates that mining missing proteins focused on cancer membrane subproteome can greatly contribute to map the whole human proteome. All data were deposited into ProteomeXchange with the identifier PXD002224.

Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling.

Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 µg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (∼15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 µg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression.

Synthesis of the heparin-based anticoagulant drug fondaparinux.

Fondaparinux, a synthetic pentasaccharide based on the heparin antithrombin-binding domain, is an approved clinical anticoagulant. Although it is a better and safer alternative to pharmaceutical heparins in many cases, its high cost, which results from the difficult and tedious synthesis, is a deterrent for its widespread use. The chemical synthesis of fondaparinux was achieved in an efficient and concise manner from commercially available D-glucosamine, diacetone α-D-glucose, and penta-O-acetyl-D-glucose. The method involves suitably functionalized building blocks that are readily accessible and employs shared intermediates and a series of one-pot reactions that considerably reduce the synthetic effort and improve the yield.

α-Glycosylation by D-glucosamine-derived donors: synthesis of heparosan and heparin analogues that interact with mycobacterial heparin-binding hemagglutinin.

Numerous biomolecules possess α-D-glucosamine as structural component. However, chemical glycosylations aimed at this backbone are usually not easily attained without generating the unwanted ß-isomer. We report herein a versatile approach in affording full α-stereoselectivity built upon a carefully selected set of orthogonal protecting groups on a D-glucosaminyl donor. The excellent stereoselectivity provided by the protecting group combination was found independent of leaving groups and activators. With the trichloroacetimidate as the optimum donor leaving group, core skeletons of glycosylphosphatidyl inositol anchors, heparosan, heparan sulfate, and heparin were efficiently assembled. The orthogonal protecting groups were successfully manipulated to further carry out the total syntheses of heparosan tri- and pentasaccharides and heparin di-, tetra-, hexa-, and octasaccharide analogues. Using the heparin analogues, heparin-binding hemagglutinin, a virulence factor of Mycobacterium tuberculosis, was found to bind at least six sugar units with the interaction notably being entropically driven.

Deuterium-isotope study on the reductive ring opening of benzylidene acetals.

Specific deuterated reference compounds were prepared to probe the stereoselectivity of the reductive ring opening of carbohydrate-based benzylidene-type acetals. AlD(3) revealed a retentive stereoselectivity probably through the rare S(N)i (internal nucleophilic substitution) mechanism. An S(N)1-like mechanism occurs in the acid-promoted regioselective BD(3)·THF- or Et(3)SiD-reductive ring opening.

Dicyanotriphenylamine-Based Polyimides as High-Performance Electrodes for Next Generation Organic Lithium-Ion Batteries.

Aromatic polyimide (PI) derivatives have recently been investigated as redox-active electrode materials for Li-ion batteries because of their high thermal stability and thermo-oxidative stability complemented by excellent solvent resistance, good electrical and mechanical properties, and chemical resistance. In this work, we report two PI derivatives from a newly synthesized 4,4'-diamino-3″,4″-dicyanotriphenylamine (DiCN-TPA) monomer and two dianhydrides, pyromellitic dianhydride (PMDA) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA); designated as TPA-PMPI and TPA-NTCPI, respectively, as electrode materials for Li-ion batteries. Characterizations of the PIs reveal excellent thermal stability and bipolar property. The incorporation of DiCN-TPA into the polymer structure resulted to a disordered chain arrangement, thus giving high glass transition temperatures (Tg). Electrochemical performance tests reveal that TPA-NTCPI cathode delivered a reversible specific capacity of 150 mAh g-1 at 0.1 A g-1 and exhibited a stability up to 1000 cycles. On the other hand, TPA-PMPI anode delivered a high specific capacity of up to 1600 mAh g-1 at 0.1 A g-1 after 100 cycles. The electrochemical performance of TPA-NTCPI cathode and TPA-PMPI anode are both among the best compared with other reported aromatic PI-based electrodes. The long cycle lifetime and excellent battery performance further suggest that TPA-NTCPI and TPA-PMPI are promising organic electrode materials for next generation Li-ion batteries.

Synthesis and optical properties of 1-alkyl-3-methylimidazolium lauryl sulfate ionic liquids.

We report the synthesis of a new series of imidazolium-based halogen-free ionic liquids 1-alkyl-3-methylimidazolium lauryl sulfates. By reacting 1-methylimidazole (MIM) with butyl, hexyl, octyl, and decyl bromides and exchanging bromide ion with lauryl sulfate anion, a series of ionic liquids [RMIM][C(12)H(25)OSO(3)] were produced. The high purity of these ionic liquids was verified with (1)H-NMR, (13)C-NMR, FT-IR and mass spectrometry (MS), demonstrating the effectiveness of this synthetic approach. Solubility test of these ionic liquids showed that they are soluble in most organic solvents except nonpolar solvents such as hexane and cyclohexane. The optical properties of [BMIM]Br and [BMIM][C(12)H(25)OSO(3)], where B refers to butyl, were examined. Both ionic liquids absorbed light in the UV region, yet essentially no absorption was recorded beyond 450 nm. Furthermore, both ionic liquids showed excitation wavelength-dependent fluorescence behavior. As an example, with an excitation wavelength of 360 nm, [BMIM][C(12)H(25)OSO(3)] showed an emission band maximum at 447 nm. Increasing the excitation wavelength to 440 nm, the emission band maximum was shifted to approximately 500 nm.