Unraveling the surface glycoprotein interaction network by integrating chemical crosslinking with MS-based proteomics

The cell plasma membrane provides a highly interactive platform for the information transfer between the inside and outside of cells. The surface glycoprotein interaction network is extremely important in many extracellular events, and aberrant protein interactions are closely correlated with various diseases including cancer. Comprehensive analysis of cell surface protein interactions will deepen our understanding of the collaborations among surface proteins to regulate cellular activity. In this work, we developed a method integrating chemical crosslinking, an enzymatic reaction, and MS-based proteomics to systematically characterize proteins interacting with surface glycoproteins, and then constructed the surfaceome interaction network. Glycans covalently bound to proteins were employed as “baits”, and proteins that interact with surface glycoproteins were connected using chemical crosslinking. Glycans on surface glycoproteins were oxidized with galactose oxidase (GAO) and sequentially surface glycoproteins together with their interactors (“prey”) were enriched through hydrazide chemistry. In combination with quantitative proteomics, over 300 proteins interacting with surface glycoproteins were identified. Many important domains related to extracellular events were found on these proteins. Based on the protein–protein interaction database, we constructed the interaction network among the identified proteins, in which the hub proteins play more important roles in the interactome. Through analysis of crosslinked peptides, specific interactors were identified for glycoproteins on the cell surface. The newly developed method can be extensively applied to study glycoprotein interactions on the cell surface, including the dynamics of the surfaceome interactions in cells with external stimuli.

Proteins interacting with glycoproteins on the cell surface were systematically characterized by integrating chemical crosslinking, enzymatic oxidation, and MS-based proteomics. The surface glycoprotein interaction network was then constructed.     

Expanding discriminative dimensions for analysis and imaging

Eliminating the contribution of interfering compounds is a key step in chemical analysis. In complex media, one possible approach is to perform a preliminary separation. However purification is often demanding, long, and costly; it may also considerably alter the properties of interacting components of the mixture (e.g. in a living cell). Hence there is a strong interest for developing separation-free non-invasive analytical protocols. Using photoswitchable probes as labelling and titration contrast agents, we demonstrate that the association of a modulated monochromatic light excitation with a kinetic filtering of the overall observable is much more attractive than constant excitation to read-out the contribution from a target probe under adverse conditions. An extensive theoretical framework enabled us to optimize the out-of-phase concentration first-order response of a photoswitchable probe to modulated illumination by appropriately matching the average light intensity and the radial frequency of the light modulation to the probe dynamics. Thus, we can selectively and quantitatively extract from an overall signal the contribution from a target photoswitchable probe within a mixture of species, photoswitchable or not. This simple titration strategy is more specifically developed in the context of fluorescence imaging, which offers promising perspectives.     

Specific surface modification of the acetylene-linked glycolipid vesicle by click chemistry

A novel glycolipid with a terminal acetylene was synthesized and used to prepare unilamellar vesicles. Using these vesicles, a convenient method was developed for the specific modification of the vesicle surface using the photoresponsive copper complex [Cu(OH(2))(cage)] as the catalyst for a click reaction.     

Constructing real-time,wash-free,and reiterative sensors for cell surface proteins using binding-induced dynamic DNA assembly

Cell surface proteins are an important class of biomarkers for fundamental biological research and for disease diagnostics and treatment. In this communication, we report a universal strategy to construct sensors that can achieve rapid imaging of cell surface proteins without any separation by using binding-induced dynamic DNA assembly. As a proof-of-principle, we developed a real-time and wash-free sensor for an important breast cancer biomarker, human epidermal growth factor receptor-2 (HER2). We then demonstrated that this sensor could be used for imaging and sensing HER2 on both fixed and live breast cancer cells. Additionally, we have also incorporated toehold-mediated DNA strand displacement reactions into the HER2 sensor, which allows for reiterating (switching on/off) fluorescence signals for HER2 from breast cancer cells in real-time.     

Conducting polyfurans by electropolymerization of oligofurans

Polyfurans have never been established as useful conjugated polymers, as previously they were considered to be inherently unstable and poorly conductive. Here, we show the preparation of stable and conducting polyfuran films by electropolymerization of a series of oligofurans of different chain lengths substituted with alkyl groups. The polyfuran films show good conductivity in the order of 1 S cm^–1, good environmental and electrochemical stabilities, very smooth morphologies (roughness 1–5 nm), long effective conjugation lengths, well-defined spectroelectrochemistry and electro-optical switching (in the Vis-NIR region), and have optical band-gaps in the range of 2.2–2.3 eV. A low oxidation potential needed for polymerization of oligofurans (compared to furan) is a key factor in achievement of improved properties of polyfurans reported in this work. DFT calculations and experiments show that polyfurans are much more rigid than polythiophenes, and alkyl substitution does not disturb backbone planarity and conjugation. The obtained properties of polyfuran films are similar or superior to the properties of electrochemically prepared poly(oligothiophene)s under similar conditions.     

Biosynthetic insights provided by unusual sesterterpenes from the medicinal herb Aletris farinosa

A series of novel sesterterpenes (2–6) have been isolated from the roots of Aletris farinosa and structurally characterized by MS, NMR, and X-ray crystallography in conjunction with computational modeling. Their structures provide new insights into the mechanisms of sesterterpene biosynthesis. Specifically, we propose with support from density functional theory computations that the configuration at a single stereocenter determines the fate of a key tetracyclic carbocationic intermediate, derived from an oxidogeranylfarnesol precursor. Whereas one epimer of the carbocation undergoes H⁺ elimination to give 6, the other undergoes a spectacular cascade of seven 1,2-methyl and hydride migrations leading to the previously unreported carbon skeleton of 5. Theoretical calculations suggest that the cascade is triggered by substrate preorganization in the enzyme active site.     

Synthesis and structural analysis of nonstoichiometric ternary fulleride K 1.5 Ba 0.25 CsC 60

The existence of cation-vacancy sites in fullerides might lead to long-range ordering and generate a new vacancy-ordered superstructure. The purpose of this work is to search whether or not long-range ordering of vacant tetrahedral sites, namely superstructure emerges in nonstoichiometric K _1.5 Ba _0.25 CsC ₆₀ fulleride. Therefore, K _1.5 Ba _0.25 CsC ₆₀ with cation-vacancy sites is synthesized using a precursor method to avoid inadequate stoichiometry control and formation of impurity phases within the target composition. For this purpose, first, phase-pure K ₆ C ₆₀ , Ba ₆ C ₆₀ and Cs ₆ C ₆₀ precursors are synthesized. Stoichiometric quantities of these precursors are used for further reaction with C ₆₀ to afford K _1.5 Ba _0.25 CsC ₆₀ . Rietveld analysis of the high-resolution synchrotron X-ray powder diffraction data of the precursors and K _1.5 Ba _0.25 CsC ₆₀ confirms that K ₆ C ₆₀ , Ba ₆ C ₆₀ and Cs ₆ C ₆₀ are single-phase and they crystallize in a body-centered-cubic structure ( Im 3) as reported in the literature. The analysis also shows that K _1.5 Ba _0.25 CsC ₆₀ phase can be perfectly modeled using a face-centered cubic structure. No new peaks appear which could have implied the appearance of a superstructure. This suggests that there is no long-range ordered arrangement of vacant tetrahedral sites in K _1.5 Ba _0.25 CsC ₆₀ .     

Simple electrochemical sensing of attomolar proteins using fabricated complexes with enhanced surface binding avidity

Various strategies have been proposed for the detection of disease protein biomarkers; however, most methods are too expensive, cumbersome or limited in sensitivity for clinical use. Here, we report that a fabricated complex can be used as a powerful tool to detect trace proteins in complex samples. In this strategy, a DNA–protein complex that comprises of one target molecule and two or more deoxyribozyme-containing probes can exhibit autonomous cleavage behavior on the surface of the substrate DNA modified electrode. In the meantime, the complex can remove the cleaved DNA fragment from the electrode surface by taking advantage of the proximity effect. The proposed approach allows one-step and highly sensitive detection of a variety of targets based on the changes of the direct electrochemical readout. Moreover, this method may also have considerable advantages over the commonly reported DNA amplification-assisted immunoassays, particularly in terms of assay simplicity and cost, which may hold great potential for application in resource-constrained regions.     

Applications of dynamic combinatorial chemistry for the determination of effective molarity

A new strategy for determining thermodynamic effective molarities (EM) for macrocylisation reactions using dynamic combinatorial chemistry under dilute conditions is presented. At low concentrations, below the critical value, Dynamic Libraries (DLs) of bifunctional building blocks contain only cyclic species, so it is not possible to quantify the equilibria between linear and cyclic species. However, addition of a monofunctional chain stopper can be used to promote the formation of linear oligomers allowing measurement of EM for all cyclic species present in the DL. The effectiveness of this approach was demonstrated for DLs generated from mixtures of 1,3-diimine calix[4]arenes, linear diaminoalkanes and monoaminoalkanes. For macrocycles deriving from one bifunctional calixarene and one diamine, there is an alternating pattern of EM values with the number of methylene units in the diamine: odd numbers give significantly higher EMs than even numbers. For odd numbers of methylene units, the alkyl chain can adopt an extended all anti conformation, whereas for even numbers of methylene units, gauche conformations are required for cyclisation, and the associated strain reduces EM. The value of EM for the five-carbon linker indicates that this macrocycle is a strainless ring.     

Synthesis of azide‐functionalized nanoparticles by microemulsion polymerization and surface modification by click chemistry in aqueous medium

Stable translucent aqueous suspensions of azide‐functionalized cross‐linked nanoparticles (NPs), with diameters in the 15–20 nm range, were prepared using two synthetic approaches. Copolymerization of azidomethylstyrene (VBN₃), styrene, and divinylbenzene in various oil‐in‐water microemulsions led to NPs with modulable azide contents (0.53–0.78 mmol/g) and surface over volume distributions. Surface modifications of reactive NPs bearing chlorobenzyl groups, produced by microemulsion copolymerization of vinylbenzylchloride, with sodium azide led to azido‐coated NPs with high densities of peripheral groups (0.13–0.45 mmol/g). It is shown that the nature of the surfactant used for the preparation of the microemulsion has an impact on the incorporation of VBN₃ in the polymer particles as well as on the surface reaction yield. The azide‐functionalized NPs were used as clickable polymeric scaffolds for the grafting of sparingly water‐soluble dansyl and fluorescein derivatives through copper(I)‐catalyzed azide‐alkyne cycloaddition in water in the presence of surfactants as solubilizing agents to produce fluorescent NPs. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Tertiary amine mediated aerobic oxidation of sulfides into sulfoxides by visible-light photoredox catalysis on TiO2

The selective oxidation of sulfides into sulfoxides receives much attention due to industrial and biological applications. However, the realization of this reaction with molecular oxygen at room temperature, which is of importance towards green and sustainable chemistry, remains challenging. Herein, we develop a strategy to achieve the aerobic oxidation of sulfides into sulfoxides by exploring the synergy between a tertiary amine and titanium dioxide via visible-light photoredox catalysis. Specifically, titanium dioxide can interact with triethylamine (TEA) to form a visible-light harvesting surface complex, preluding the ensuing selective redox reaction. Moreover, TEA, whose stability was demonstrated by a turnover number of 32, plays a critical role as a redox mediator by shuttling electrons during the oxidation of sulfide. This work suggests that the addition of a redox mediator is highly functional in establishing visible-light-induced reactions via heterogeneous photoredox catalysis.     

Surface modification of UV‐cured epoxy resins by click chemistry

A novel method for surface modification of UV‐cured epoxy network was described. Photoinitiated cationic copolymerization of a bisepoxide, namely 3,4‐epoxy cyclohexylmethyl 3,4‐epoxycyclohexanecarboxylate (EEC) with epibromohydrine (EBH) by using a cationic photoinitiator, [4‐(2‐methylpropyl)phenyl]4‐methylphenyl‐iodonium hexafluorophosphate, in propylene carbonate solution was studied. The real‐time Fourier transform infrared spectroscopic, gel content determination and thermal characterization studies revealed that both EEC and EBH monomers take part in the polymerization and epoxy network possessing bromomethyl functional groups was obtained. The bromine functions of the cured product formed on the glass surface were converted to azide functionalities with sodium azide. Independently prepared alkyne functional poly(ethylene glycol) (PEG) was subsequently anchored to azide‐modified epoxy surface by a “click” reaction. Surface modification of the network through incorporation of hydrophilic PEG chain was evidenced by contact angle measurements. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2862–2868, 2010     

Synthesis of Boltorn 1,2,3‐triazole dendrimers by click chemistry

Second‐, third‐, and fourth‐generation hyperbranched aliphatic polyols namely Boltorn® H20, Boltorn H30, and Boltorn H40 were endcapped with azido and activated acetylenic groups in good to excellent yields (75–95%) following an acid catalyzed procedure. The resultant terminally functionalized dendritic azido and acetylenic groups undergo 1,3‐dipolar cycloaddition using methyl (or ethyl) propiolate and benzyl azide, respectively, under catalytic or noncatalytic conditions below 40 °C to yield 1,2,3‐triazole dendrimeric polymers in 82–95% yield, under extremely mild conditions that could be applied for compounds sensitive to acid, base, or heat. The dendritic azido and activated acetylenic derivatives may act as novel scaffolds to tune the mechanical properties of different polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3748–3756, 2009     

High-throughput imaging assay of multiple proteins via target-induced DNA assembly and cleavage

This work integrates target-induced DNA assembly and cleavage on a DNA chip to design a versatile imaging strategy as an assay for multiple proteins. The DNA assembly is achieved via immunological recognition to trigger the proximity hybridization for releasing a DNA sequence, which then hybridizes with FITC-DNA1 immobilized on the chip to induce the enzymatic cleavage of DNA1 and thus decrease the signals. The signal readout is performed with both fluorescent imaging of the left FITC and chemiluminescent (CL) imaging, by adding peroxidase labelled anti-FITC in assembly solution and CL substrates to produce CL emission. This one-step incubation can be completed in 30 min. The imaging method shows wide detection ranges and detection limits down to pg mL^–1 for the simultaneous detection of 4 protein biomarkers. This high-throughput strategy with good practicability can be easily extended to other protein analytes, providing a powerful protocol for protein analysis and clinical diagnosis.     

Effect of water addition on the coupling of homopolymers by click chemistry

Homopolymers bearing terminal azide and alkyne groups can be coupled via click chemistry to yield diblock copolymers. When performed in solvents that dissolved both homopolymers, the click reaction was found in this study to be inefficient, probably due to the embedding of the reactive end groups inside the random coils of the polymers. The efficiency was only slightly affected by the addition of a small amount of water into the reaction mixture. However, the reaction efficiency increased dramatically near the water volume fraction where one or both of the reacting polymers began to precipitate. Further increases in water content caused the polymer(s) to undergo macroscopic phase separation and the click reaction efficiency decreased once again. A possible explanation for the observed effect of water on the polymer coupling reaction is proposed. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

An approach for the surface functionalized gold nanoparticles with pH-responsive polymer by combination of RAFT and click chemistry

In this report, we demonstrated a novel efficient post-modification route for preparation of smart hybrid gold nanoparticles with poly(4-vinylpyridine) (P4VP) based on RAFT and click chemistry. A new azide terminated ligand was first synthesized to modify gold nanoparticles by ligand exchange reaction, and then click reaction was used to graft alkyne terminated P4VP which was prepared by RAFT onto the surface of gold nanoparticles. The functionalized hybrid gold nanoparticles were characterized by TEM, FTIR, and XPS etc. The results indicated that the P4VP was successfully grafted onto the surface of gold nanoparticles by click reaction. The surface grafting density was calculated to be about 6 chains/nm²_. In addition, the hybrid gold nanoparticles showed a pH responsive phenomenon as the pH value changed around 5.     

In situ activation and monitoring of the evolution of the intracellular caspase family

The evolution of the intracellular caspase family is crucial in cell apoptosis. To evaluate this process, a universal platform of in situ activation and monitoring of the evolution of intracellular caspase is designed. Using well-known gold nanostructure as a model of both nanocarrier and matter inducing the cell apoptosis for photothermal therapy, a nanoprobe is prepared by assembly of two kinds of dye-labelled peptides specific to upstream caspase-9 and downstream caspase-3 as the signal switch, and folic acid as a targeting moiety. The energy transfer from dyes to the gold nanocarrier at two surface plasmon resonance absorption wavelengths leads to their fluorescence quenching. Upon endocytosis of the nanoprobe to perform the therapy against cancer cells, the peptides are successively cleaved by intracellular caspase activation with the evolution from upstream to downstream, which lights up the fluorescence of the dyes sequentially, and can be used to quantify both caspase-9 and caspase-3 activities in cancer cells and to monitor their evolution in living mice. The recovered fluorescence could also be used to assess therapeutic efficiency. This work provides a novel powerful tool for studying the evolution of the intracellular caspase family and elucidating the biological roles of caspases in cancer cell apoptosis.     

Humidity-dependent surface tension measurements of individual inorganic and organic submicrometre liquid particles

Surface tension, an important property of liquids, is easily measured for bulk samples. However, for droplets smaller than one micron in size, there are currently no reported measurements. In this study, atomic force microscopy (AFM) and force spectroscopy have been utilized to measure surface tension of individual submicron sized droplets at ambient pressure and controlled relative humidity (RH). Since the surface tension of atmospheric aerosols is a key factor in understanding aerosol climate effects, three atmospherically relevant systems (NaCl, malonic and glutaric acids) were studied. Single particle AFM measurements were successfully implemented in measuring the surface tension of deliquesced particles on the order of 200 to 500 nm in diameter. Deliquesced particles continuously uptake water at high RH, which changes the concentration and surface tension of the droplets. Therefore, surface tension as a function of RH was measured. AFM based surface tension measurements are close to predicted values based on bulk measurements and activities of these three chemical systems. Non-ideal behaviour in concentrated organic acid droplets is thought to be important and the reason for differences observed between bulk solution predictions and AFM data. Consequently, these measurements are crucial in order to improve atmospheric climate models as direct measurements hitherto have been previously inaccessible due to instrument limitations.     

Accurate molecular weight determination of small molecules via DOSY-NMR by using external calibration curves with normalized diffusion coefficients

Determination of the aggregation and solvation numbers of organometallic complexes in solution is an important task to increase insight in reaction mechanisms. Thus knowing which aggregates are formed during a reaction is of high interest to develop better selectivity and higher yields. Diffusion-ordered spectroscopy (DOSY), which separates NMR signals according to the diffusion coefficient, finds increasing use to identify species in solution. However, there still is no simple relationship between diffusion coefficient and molecular weight (MW). Some methods have been developed to estimate the MW but still with a significant error of ±30%. Here we describe a novel development of MW-determination by using an external calibration curve (ECC) approach with normalized diffusion coefficients. Taking the shape of the molecules into account enables accurate MW-predictions with a maximum error of smaller than ±9%. Moreover we show that the addition of multiple internal references is dispensable. One internal reference (that also can be the solvent) is sufficient. If the solvent signal is not accessible, 16 other internal standards (aliphatics and aromatics) are available to avoid signal overlapping problems and provide flexible choice of analytes. This method is independent of NMR-device properties and diversities in temperature or viscosity and offers an easy and robust method to determine accurate MWs in solution.     

In situ formation of a biomimetic lipid membrane triggered by an aggregation-enhanced photoligation chemistry

Nature or synthetic systems that can self-assemble into biomimetic membranes and form compartments in aqueous solution have received extensive attention. However, these systems often have the problems of requiring complex processes or lacking of control in simulating lipid synthesis and membrane formation of cells. This paper demonstrates a conceptually new strategy that uses a photoligation chemistry to convert nonmembrane molecules to yield liposomes. Lysosphingomyelin (Lyso) and 2-nitrobenzyl alcohol derivatives (NBs) are used as precursors and the amphiphilic character of Lyso promotes the formation of mixed aggregates with NBs, bringing the lipid precursors into close proximity. Light irradiation triggers the conversion of NBs into reactive aldehyde intermediates, and the preassembly facilitates the efficient and specific ligation between aldehyde and Lyso amine over other biomolecules, thereby accelerating the synthesis of phospholipids and forming membrane compartments similar to natural lipids. The light-controllable transformation represents the use of an external energy stimulus to form a biomimetic phospholipid membrane, which has a wide range of applications in medicinal chemistry, synthetic biological and abiogenesis.

A photoligation chemistry was used to drive the formation of biomimetic membranes in situ. The preassembly of precursors promotes the synthesis of lipid, which is an important feature as a candidate for simulating natural membrane functions.