A new algorithm for construction of coarse‐grained sites of large biomolecules

The development of coarse‐grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary‐constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F‐actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.     

Facile preparation of a high‐capacity boronate‐affinity adsorbent based on low‐cost commercial supports for selective enrichment of cis‐diol‐containing biomolecules

Boronate‐affinity adsorbents have been regarded as favorable extraction adsorbents for the pretreatment of cis‐diol‐containing biomolecules owning to their specific selectivity, but most of them have low adsorption capacity and a tedious synthesis methods. In this study, a new boronate‐affinity material (PGMA@FPBA) with high adsorption capacity was synthesized via a “one‐pot” method based on a low‐cost commercial support. The PGMA@FPBA was characterized by Fourier transform infrared spectroscopy (FT‐IR), X‐ray photoelectron spectroscopy (XPS), scanning electron microscope (SEM), and nitrogen adsorption/desorption measurements. The as‐prepared adsorbent showed good selectivity, high adsorption capacity (448 μmol/g for catechol), and fast adsorption equilibration (1 min) for cis‐diol‐containing biomolecules. Subsequently, as an example for application, the obtained PGMA@FPBA was used as a dispersive solid‐phase extraction (d‐SPE) adsorbent for enrichment of quercetin in red wine. The results indicated that the facile‐prepared boronate‐affinity adsorbent has great potential application for separation and enrichment of cis‐diol‐containing biomolecules in complex samples.     

Double‐Layer Nanogold and Double‐Strand DNA‐Modified Electrode for Electrochemical Immunoassay of Cancer Antigen 15‐3

Various sensor‐based immunoassay methods have been extensively developed for the detection of cancer antigen 15‐3 (CA 15‐3), but most often exhibit low detection signals and low detection sensitivity, and are unsuitable for routine use. The aim of this work is to develop a simple and sensitive electrochemical immunoassay for CA 15‐3 in human serum by using nanogold and DNA‐modified immunosensors. Prussian blue (PB), as a good mediator, was initially electrodeposited on a gold electrode surface, then double‐layer nanogold particles and double‐strand DNA (dsDNA) with the sandwich‐type architecture were constructed on the PB‐modified surface in turn, and then anti‐CA 15‐3 antibodies were adsorbed onto the surface of nanogold particles. The double‐layer nanogold particles provided a good microenvironment for the immobilization of biomolecules. The presence of dsDNA enhanced the surface coverage of protein, and improved the sensitivity of the immunosensor. The performance and factors influencing the performance of the immunosensor were evaluated. Under optimal conditions, the proposed immunosensor exhibited a wide linear range from 1.0 to 240 ng/mL with a relatively low detection limit of 0.6 ng/mL (S/N=3) towards CA 15‐3. The stability, reproducibility and precision of the as‐prepared immunosensor were acceptable. 57 serum specimens were assayed by the developed immunosensor and standard enzyme‐linked immunosorbent assay (ELISA), respectively, and the results obtained were almost consistent. More importantly, the proposed methodology could be further developed for the immobilization of other proteins and biocompounds.     

Voltammetry of Undiluted Red‐Ox Systems. Electrochemical ESR‐ and Electrochemical Impedance Spectroscopy Evidence for Formation of Ionic Liquid at Microelectrode Surface

It is believed that voltammetry of undiluted red‐ox liquids can lead to the formation of stable thin layers of ionic liquids at the microelectrode surface. Such situation was postulated for several liquids (solvents), however, so far no hard evidence supporting this expectation was obtained. By using electron spin resonance in combination with voltammetric experiments and electrochemical impedance spectroscopy we have shown that the concentration of the cation radicals at the microelectrode surface may be high (nitrobenzene) and the overall resistance of the solution abruptly drops (methanol) when the potential at the microelectrode corresponds to the wave plateau of the undiluted organic liquid. Both facts constitute a good evidence for the formation of microlayers of ionic liquids at the microelectrode surface during electrolysis of undiluted red‐ox systems.     

Electrochemical Treatment of Glassy Carbon for Label‐Free Detection of DNA Bases and Neurotransmitters

Electrochemically reduced glassy carbon (r‐GC) showed a superior electrochemical sensing performance, compared to oxidized GC (ox‐GC) and untreated GC for the oxidation of 4 DNA bases and neurotransmitters (epinephrine, norepinephrine and serotonin). r‐GC exhibited not only the largest current intensities of all redox biomolecules, but also displayed an excellent selectivity in detecting coexisting redox biomolecules. The enhanced performance of r‐GC was attributed to the improved surface cleanliness of electrode and its catalytic surface functional groups. The results presented herein imply that simple electrochemical treatments are a viable method to produce sensitive and selective electrodes for label‐free biosensing.     

Preparation of GOD/Sol‐Gel Silica Film on Prussian Blue Modified Electrode for Glucose Biosensor Application

A novel amperometric glucose biosensor was fabricated by in situ incorporating glucose oxidase (GOD) within the sol‐gel silica film on a Prussian blue (PB) modified electrode. The method is simple and controllable, which combined the merits of in situ immobilizing biomolecules in sol‐gel silica film by electrochemical method and the synergic catalysis effects of PB and GOD molecules. Scanning electron microscopy (SEM) showed that the GOD/sol‐gel silica film was homogeneous with a large number of three‐dimensional nanopores, which not only enhanced mass transport, but also maintained the active configuration of the enzyme molecule and prevented the leakage of enzyme, therefore improved the stability and sensitivity of the biosensor. The fabricated biosensor showed fast response time (10 s), high sensitivity (26.6 mA cm^?2 M^?1), long‐term stability, good suppression of interference, and linear range of 0.01 mM–5.8 mM with a low detection limit of 0.94 μM for the detection of glucose. In addition, the biosensor was successfully applied to determine glucose in human serum samples.     

Comparison of various silica‐based monoliths for the analysis of large biomolecules†

In the present study, three types of silica‐based monoliths, i.e. the first and second generations of commercial silica monolithic columns and a wide‐pore prototype monolith were compared for the analysis of large biomolecules. These molecules possess molecular weights between 1 and 66 kDa. The gradient kinetic performance of the first‐generation monolith was lower than that of the second generation, for large biomolecules (>14 kDa) but very close with smaller ones (1.3–5.8 kDa). In contrast, the wide‐pore prototype column was particularly attractive with proteins larger than 19 kDa (higher peak capacity). Among these three columns, the selectivity and retention remained quite similar but a possible larger number of accessible and charged residual silanols was noticed on the wide‐pore prototype material, which led to unpredicted small changes in selectivity and slightly broader peaks than expected. The peak shapes attained with the addition of 0.1% formic acid in the mobile phase remained acceptable for MS coupling, particularly for biomolecules of less than 6 kDa. It was found that one of the major issues with all of these silica‐based monoliths is the possible poor recovery of large biomolecules (principally with monoclonal antibody fragments of more than 25 kDa).     

Biomolecule‐Doped Organic/Inorganic Hybrid Nanocomposite Film for Label‐Free Electrochemical Immunoassay of α‐1‐Fetoprotein

A new electrochemical immunosensor for the detection of α‐1‐fetoprotien (AFP) was developed based on AFP antibody (anti‐AFP)‐functionalized organic/inorganic hybrid nanocomposite membrane. To fabricate such a hybrid composite membrane, 3,4,9,10‐perylenetetracarboxylic acid‐bound thionine molecules (PTCTH) were initially doped into titania colloids (TiO₂), and then gold nanoparticles and anti‐AFP were immobilized onto the composite film in turn. Comparison with the electrode fabricated only with thionine not 3,4,9,10‐perylenetetracarboxylic acid, the immunosensor with PTCTH exhibited high sensitivity and fast electron transfer. The presence of gold nanoparticles provided a good microenvironment for the immobilization of biomolecules, enhanced the surface coverage of protein, and improved the sensitivity of the immunosensor. The modified process was characterized by scanning electron microscope (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The surface topography of the membrane was investigated by scanning electron microscopy (SEM). Under optimal conditions, the proposed immunosensor exhibited a wide linear range from 2.5 to 200.0 ng/mL towards AFP with a detection limit of 0.5 ng/mL (S/N=3). The stability, reproducibility and precision of the immunosensor were acceptable. Comparison with the conventional enzyme‐linked immunosorbent assay (ELISA), the present method did not require more labeled procedures and washing steps. Significantly, the detection methodology provides a promising approach for other proteins or biosecurities.     

In‐capillary self‐assembly study of quantum dots and protein using fluorescence coupled capillary electrophoresis

As a vast number of novel materials in particular inorganic nanoparticles have been invented and introduced to all aspects of life, public concerns about how they might affect our ecosystem and human life continue to arise. Such incertitude roots at a fundamental question of how inorganic nanoparticles self‐assemble with biomolecules in solution. Various techniques have been developed to probe the interaction between particles and biomolecules, but very few if any can provide advantages of both rapid and convenient. Herein, we report a systematic investigation on quantum dots (QDs) and protein self‐assembly inside a capillary. QDs and protein were injected to a capillary one after another. They were mixed inside the capillary when a high voltage was applied. Online separation and detection were then achieved. This new method can also be used to study the self‐assembly kinetics of QDs and protein using the Hill equation, the K_D value for the self‐assembly of QDs and protein was calculated to be 8.8 μM. The obtained results were compared with the previous out of‐capillary method and confirmed the effectiveness of the present method.     

3,3′‐Diamino‐N‐methyldipropylamine as a versatile affinity ligand

Currently, in biomedicine and biotechnology fields, there is a growing need to develop and produce biomolecules with a high degree of purity. To accomplish this goal, new purification methods are being developed looking for higher performance, efficiency, selectivity, and cost‐effectiveness. Affinity chromatography is considered one of the most highly selective methods for biomolecules purification. The purpose of this work is to explore a new type of a structurally simple ligand immobilized onto an agarose matrix to be used in affinity chromatography. The ligand in this study, 3,3′‐diamino‐N‐methyldipropylamine has shown low toxicity and low cost of preparation. Moreover, the ability of the ligand to be used in affinity chromatography to purify proteins and nucleic acids was verified. An increasing sodium chloride gradient, using salt concentrations up to 500 mM, was suitable to accomplish the purification of these biomolecules, meaning that the new support allows the recovery of target biomolecules under mild conditions. Thus, the 3,3′‐diamino‐N‐methyldipropylamine ligand is shown to be a useful and versatile tool in chromatographic experiments, with very good results either for proteins or supercoiled plasmid isoform purification.     

Novel synthetic route for covalent coupling of biomolecules on super‐paramagnetic hybrid nanoparticles

The immobilization of biomolecules on magnetic nanoparticles is an issue with high potential in different fields. We describe herein a new strategy to immobilize biomolecules on super‐paramagnetic nanoparticles based on the reactivity of vinyl sulfone groups with naturally occurring functional groups present in biomolecules (amine and thiol). A new monomer containing a polymerizable methacryloyl group and a secondary amine group was synthesized and used to prepare super‐paramagnetic hybrid nanoparticles (SP‐HNPs) by two‐step miniemulsion polymerization. The Michael addition reaction of divinyl sulfone (DVS) to the secondary amine groups localized on the nanoparticles surface allows the introduction of the vinyl sulfone function in the SP‐HNPs (SP‐HNPs‐VS). The morphology of the functionalized SP‐HNPs was characterized by transmission electron microscopy (TEM), high‐resolution transmission electron microscopy (HRTEM), dynamic light scattering, and magnetic susceptibility. The capacity of SP‐HNPs‐VS for the immobilization of biomolecules was evaluated with three model proteins: avidin, invertase, and horseradish peroxidase (HRP). The model proteins were successfully immobilized in mild aqueous conditions compatible with the biological nature of the enzymes. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Crystalline β‐structure of PHBV grown epitaxially on silicate layers of MMT

The poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) (PHBV)/montmorillonite(MMT) nanocomposites were investigated by wide‐angle X‐ray scattering (WAXS). The aim of the investigation was solution intercalation of MMT with PHBV. Beside the usual orthorhombic unit cell, a stable pseudohexagonal β‐structure of PHBV was obtained. Well known β‐structure has one common WAXS reflection (d = 0.480 nm), which corresponds to the mean distance of PHBV chains in the pseudohexagonal structure. The new β‐structure has two diffraction peaks in the WAXS pattern. It is a three‐dimensionally ordered crystalline structure oriented in parallel with the silica layers of MMT. The new polymorphic form is supposed to be growing on the layers of MMT. Its layers serve as primary nucleation centers for epitaxial growth of the β‐structure. After annealing, this polymorphic form of PHBV disappears and it is transformed into the more stable α‐form leading to an enhanced total crystallinity of the polymer comprised in the nanocomposite. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 751–755, 2009     

Syntheses,Structures, and Electrochemical Properties of Two Bis‐triazole‐bis‐amide‐based Copper(II) Pyridine‐2,3‐dicarboxylate Coordination Polymers

Abstract. Two bis‐triazole‐bis‐amide‐based copper(II) pyridine‐2,3‐dicarboxylate coordination polymers (CPs), [Cu(2,3‐pydc)(dtb)_0.5(DMF)] · 2H₂O ( 1 ) and [Cu(2,3‐pydc)(dth)_0.5(DMF)] · 2H₂O ( 2 ) (2,3‐H₂pydc = pyridine‐2,3‐dicarboxylic acid, dtb = N,N′‐bis(4H‐1,2,4‐triazole)butanamide, and dth = N,N′‐bis(4H‐1,2,4‐triazole)hexanamide), were synthesized under solvothermal conditions. CPs 1 and 2 show similar two‐dimensional (2D) structures. In 1 , the 2,3‐pydc anions bridge the Cu^II ions into a one‐dimensional (1D) chain. Such 1D chains are linked by the dtb ligands to form a 2D layer. The adjacent 2D layers are extended into a three‐dimensional (3D) supramolecular architecture by hydrogen‐bonding interactions. The electrochemical properties of 1 and 2 were investigated.     

Surface‐Assisted Laser Desorption/Ionization Mass Spectrometric Detection of Biomolecules by Using Functional Single‐Walled Carbon Nanohorns as the Matrix

A surface‐assisted laser desorption/ionization time‐of‐flight mass spectrometric (SALDI‐TOF MS) method was developed for the analysis of small biomolecules by using functional single‐walled carbon nanohorns (SWNHs) as matrix. The functional SWNHs could transfer energy to the analyte under laser irradiation for accelerating its desorption and ionization, which led to low matrix effect, avoided fragmentation of the analyte, and provided high salt tolerance. Biomolecules including amino acids, peptides, and fatty acids could successfully be analyzed with about 3‐ and 5‐fold higher signals than those obtained using conventional matrix. By integrating the advantages of SWNHs and the recognition ability of aptamers, a selective approach was proposed for simultaneous capture, enrichment, ionization, and MS detection of adenosine triphosphate (ATP). This method showed a greatly improved detection limit (1.0 μM ) for the analysis of ATP in complex biological samples. This newly designed protocol not only opened a new application of SWNHs, but also offered a new technique for selective MS analysis of biomolecules based on aptamer recognition systems.     

Polymer‐Based Surfaces Designed to Reduce Biofilm Formation: From Antimicrobial Polymers to Strategies for Long‐Term Applications

Contact‐active antimicrobial polymer surfaces bear cationic charges and kill or deactivate bacteria by interaction with the negatively charged parts of their cell envelope (lipopolysaccharides, peptidoglycan, and membrane lipids). The exact mechanism of this interaction is still under debate. While cationic antimicrobial polymer surfaces can be very useful for short‐term applications, they lose their activity once they are contaminated by a sufficiently thick layer of adhering biomolecules or bacterial cell debris. This layer shields incoming bacteria from the antimicrobially active cationic surface moieties. Besides discussing antimicrobial surfaces, this feature article focuses on recent strategies that were developed to overcome the contamination problem. This includes bifunctional materials with simultaneously presented antimicrobial and protein‐repellent moieties; polymer surfaces that can be switched from an antimicrobial, cell‐attractive to a cell‐repellent state; polymer surfaces that can be regenerated by enzyme action; degradable antimicrobial polymers; and antimicrobial polymer surfaces with removable top layers.     

A microfluidic glucose sensor incorporating a novel thread‐based electrode system

An electrochemical sensor for the detection of glucose using thread‐based electrodes and fabric is described. This device is relatively simple to fabricate and can be used for multiple readings after washing with ethanol. The fabrication of the chip consisted of two steps. First, three thread‐based electrodes (reference, working, and counter) were fabricated by painting pieces of nylon thread with either layered silver ink and carbon ink or silver/silver chloride ink. The threads were then woven into a fabric chip with a beeswax barrier molded around the edges in order to prevent leaks from the tested solutions. A thread‐based working electrode consisting of one layer of silver underneath two layers of carbon was selected to fabricate the final sensor system. Using the chip, a PBS solution containing glucose oxidase (GOx) (10 mg/mL), potassium ferricyanide (K₃[Fe(CN)₆]) (10 mg/mL) as mediator, and different concentrations of glucose (0‐25 mM), was measured by cyclic voltammetry (CV). It was found that the current output from the oxidation of glucose was proportional to the glucose concentrations. This thread‐based electrode system is a viable sensor platform for detecting glucose in the physiological range.     

Fabrication of Au‐Nanoparticle/TiO2‐Nanotubes Electrodes Using Electrochemical Methods and Their Application for Electrocatalytic Oxidation of Hydroquinone

Gold nanoparticle (Au‐NPs)‐Titanium oxide nanotube (TiO₂‐NTs) electrodes are prepared by using galvanic deposition of gold nanoparticles on TiO₂‐NTs electrodes as support. Scanning electron microscopy and energy‐dispersive X‐ray spectroscopy results indicate that nanotubular TiO₂ layers consist of individual tubes of about 60–90 nm diameters and gold nanoparticles are well‐dispersed on the surface of TiO₂‐NTs support. The electrooxidation of hydroquinone of Au‐NPs/TiO₂‐NTs electrodes is investigated by different electrochemical methods. Au‐NPs/TiO₂‐NTs electrode can be used repeatedly and exhibits stable electrocatalytic activity for the hydroquinone oxidation. Also, determination of hydroquinone in skin cream using this electrode was evaluated. Results were found to be satisfactory and no matrix effects are observed during the determination of hydroquinone content of the “skin cream” samples.     

Light‐Triggered Capture and Release of DNA and Proteins by Host–Guest Binding and Electrostatic Interaction

The development of an effective and general delivery method that can be applied to a large variety of structurally diverse biomolecules remains a bottleneck in modern drug therapy. Herein, we present a supramolecular system for the dynamic trapping and light‐stimulated release of both DNA and proteins. Self‐assembled ternary complexes act as nanoscale carriers, comprising vesicles of amphiphilic cyclodextrin, the target biomolecules and linker molecules with an azobenzene unit and a charged functionality. The non‐covalent linker binds to the cyclodextrin by host–guest complexation with the azobenzene. Proteins or DNA are then bound to the functionalized vesicles through multivalent electrostatic attraction. The photoresponse of the host–guest complex allows a light‐induced switch from the multivalent state that can bind the biomolecules to the low‐affinity state of the free linker, thereby providing external control over the cargo release. The major advantage of this delivery approach is the wide variety of targets that can be addressed by multivalent electrostatic interaction, which we demonstrate on four types of DNA and six different proteins.     

Preparation of few‐layer two‐dimensional polymers by self‐assembly of bola‐amphiphilic small molecules

Two bola‐amphiphilic small molecules, based on the diphenylanthracene skeleton structure, namely, BASM‐1 and its functionalized small molecule BASM‐2 , were designed and synthesized. The self‐assembly behavior and mechanism of these two molecules in aqueous solution were studied. The supramolecular two‐dimensional (2D) layer and the covalent 2D polymers were, respectively, prepared by these two molecules. What is more, the transverse size of the covalent 2D polymer laminates increased with the extension of the polymerization time. Atomic force microscopy results showed that both free‐standing single‐layer 2D polymers and few layer laminates with two to three molecular layers were obtained. So our work provides a simple and efficient method for directly preparing independent both supramolecular 2D polymers and covalent 2D polymers in liquid phase which is of great significance. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1748–1755     

Preparation of Organophilic Nanohybrid Kaolinite and Application to the Electrochemical Detection of Organic Pesticide

Novel organophilic nanohybrid materials (K‐TDD) were obtained by the grafting of 1,2‐tetradecanediol (TDD) onto the surface of kaolinite (K). XRD, IR, TGA‐DTG, and SEM characterization showed that TDD grafting results in a partial exfoliation of kaolinite layers. This material was used to modify a glassy carbon electrode (GCE/K‐TDD) and applied for the trace analysis of methyl parathion (MP). The signal of MP recorded on GCE/K‐TDD was more intense compared to the unmodified GCE or to one modified with a film of natural kaolinite. Several parameters that can affect the stripping response were systematically investigated to optimize the sensitivity of the organokaolinite‐modified electrode. A linear calibration curve for MP was obtained in the concentration range from 2×10⁻⁶ to 14×10⁻⁶ mol .L⁻¹ in acetate buffer (pH 6), giving a detection limit of 9×10⁻⁸ mol .L⁻¹. The sensitivity of the method was found to be 2.42 μA/μM for the range of concentrations that gives a linear calibration curve. The electrode was shown to be very stable, with the electrochemical response of MP decreasing by only 1.5 % after a series of nine measurements. The interference of various inorganic ions and organic compounds likely to influence the stripping determination of the MP were also examined. The results showed that the GCE/K‐TDD electrode was effective in solutions containing interfering species and could be applied for the quantification of MP pesticide in natural water.