Effect of the sarcosine residue on sequence scrambling in peptide b5 ions

The effect of N‐methylation on sequence scrambling in the fragmentation of b₅ ions has been investigated by studying a variety of peptides containing sarcosine (N‐methylglycine). The product ion mass spectra for the b₅ ions derived from Sar‐A‐A‐A‐Y‐A and Sar‐A‐A‐Y‐A‐A show only minor signals for non‐direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b₅ ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b₅ ion derived from Y‐Sar‐A‐A‐A‐A shows a product ion mass spectrum essentially identical to the spectrum of the b₅ ion derived from Sar‐A‐A‐A‐Y‐A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N‐terminal position. Similar results were obtained in the comparison of b₅ ions derived from A‐Sar‐A‐A‐Y‐A and Sar‐A‐A‐Y‐A‐A. The product ion mass spectra of the MH⁺ ions of Y‐Sar‐A‐A‐A‐A and A‐Sar‐A‐A‐Y‐A show substantial signals for non‐direct sequence ions indicating that fragmentation of the MH⁺ ions channels extensively through the respective b₅ ions and further fragmentation of these species. Copyright © 2014 John Wiley & Sons, Ltd.     

Development of a Microsphere-Based Immunoassay Authenticating A2 Milk and Species Purity in the Milk Production Chain

Processed milk and milk products produced from bovine milk, commonly contain β-casein A1 (βCA1) and β-casein A2 (βCA2). Since the presence of βCA1 is linked to milk intolerance and digestion problems, A2A2 milk, which only contains βCA2, is proposed as a healthier alternative. To support this health claim, the purity of A2A2-milk has to be guaranteed. In the presented study, a multiplex immunoassay, able to distinguish between βCA2 and βCA1, was developed and real-life applicability was shown on raw milk samples from genotyped A1A1, A1A2 and A2A2 cows. Because of its ability to discriminate between βCA2 and βCA1, this newly developed method was able to detect the addition of common bovine A1A2 milk to A2A2 milk, as low as 1%. Besides the detection of A2A2 milk purity, the developed assay can also be implemented as a rapid phenotyping method at dairy farms to replace the more invasive DNA-based screening. Additionally, the developed method was capable of detecting the addition of common bovine milk up to 1% in sheep, goat, buffalo, horse and donkey milk, which conforms to EU recommendations. In conclusion, a newly developed multiplex method capable of reliably detecting the dilution of A2A2 milk of multiple species, with common bovine milk up to 1%, is presented.     

中成药中马兜铃酸A的HPLC/MS分析方法

建立了中成药中马兜铃酸A的高效液相色谱/质谱检测方法.测定结果表明,马兜铃酸A的质谱有较强的分子离子峰,最低检测限为5 ng(信噪比等于10),可以满足对中成药中马兜铃酸A测定之要求.     

A correlated force-optical study on the self-assembly behavior of annexin V on model membranes: effect of dye conjugation

We have examined the self-assembled membrane-bound aggregates of two annexin V (A5) dye conjugates and compared them to those from native A5. Native A5 and FITC-labeled A5 (A5-FITC) both formed discrete well-defined crystalline monolayer domains of p6 symmetry. However, A5-FITC also showed additional domains with a corrugated appearance not observed in native A5. In contrast, Cy3-labeled A5 (A5-Cy3) showed a mixture of crystalline monolayer and irregular multilayered domains, with the ratio of the two types varying significantly from sample to sample, and also required a much longer incubation time than native A5 and A5-FITC. When A5-FITC and A5-Cy3 were co-incubated on the same bilayer, well-defined crystalline monolayer domains containing both A5-FITC and A5-Cy3 were consistently observed at a much shorter incubation time than that of pure A5-Cy3 alone, indicating that A5-FITC facilitates the inclusion of A5-Cy3. These results suggest that dye labels can affect A5 2D self-assembly and crystal formation on membrane surfaces.     

Two-dimensional lattice Monte Carlo simulation of the compatibility of A/B/functionalized A ternary polymer mixtures coupled with chemical reaction

Compatibility of A/B and functionalized A ternary polymer mixtures was studied by Monte Carlo simulation in a two-dimensional lattice. Polymer A was a nonreactive polymer, whereas polymer B was a reactive polymer and immiscible with polymer A. Functionalized polymer A could react with the end group of polymer B, leading to the formation of block copolymers. Simulation results showed the phase domain sizes dropped considerably with increasing functionalized polymer A content, indicating that the compatibility between polymer A and B could be markedly improved with the introduction of functionalized polymer A. Moreover, it was shown that the resulting block copolymers tended to distribute at the phase interface between polymer A and B, and the block copolymer conformation depended on the structures of polymer B and functionalized polymer A. In case 1, i.e., both polymer B and functionalized polymer A were with single end group, it could be found that the block A and block B of resulting A–B copolymer inserted into polymer A and polymer B phase domains, respectively. In case 2, i.e., functionalized polymer A was with single end group and polymer B was with double end groups, it was found that the resulting A–B–A triblock copolymer tended to connect two neighbor separated polymer A phase domains. However, in case 3, namely functionalized polymer A was with double end groups and polymer B was with single end group, it was found that the resulting B–A–B triblock copolymer was likely to form a folding conformation. These lead to the different compatibilizing effects for different polymer structures. Comparing with case 1 and case 2, functionalized polymer A with double end groups (case 3) had less effective to compatibilize the A/B polymer blends. For the purpose of comparison, same simulations were carried out in a three-dimensional lattice. The results showed the compatibility behavior of the mixtures was similar to those in the two-dimensional lattice with the addition of functionalized polymer A. However, the conformation of the resulting block copolymers was different from that in the two-dimensional lattice.     

Synthesis and Characterization of Water‐Soluble Conjugated Glycopolymer for Fluorescent Sensing of Concanavalin A

A neutral polyfluorene derivative that contains 20 mol % 2,1,3‐benzothiadiazole (BT) is synthesized by Suzuki cross‐coupling polymerization. A cationic conjugated polymer A and an α‐mannose‐bearing polymer B are subsequently obtained through different post‐polymerization methods. As a result of the charged pendant groups or sugar‐bearing groups attached to the polymer side chains, both A and B show good water‐solubility. The titration of Concanavalin A (Con A) into polymer aqueous solution leads to different fluorescent responses for polymers A and B . Polymer A does not show any obvious fluorescence change upon interaction with Con A, whereas polymer B shows fluorescence increase in BT emission intensity when Con A is added. This is because of the specific interaction between α‐mannose and Con A, which induces polymer aggregation, and then facilitates energy transfer from the phenylene–fluorene segments to the BT units. A practical calibration curve ranging from 1 nM to 250 nM is obtained by correlating the changes in BT emission intensity with Con A concentration. The advantage of polymer B ‐based Con A macromolecular probe is that it shows signal increase upon Con A recognition, which is significantly different from other conjugated polymer‐based fluorescence quenching assays.     

A2-rhodopsin: a new fluorophore isolated from photoreceptor outer segments

A2E and iso-A2E are fluorescent amphiphilic pyridinium bisretinoids involved in age-related macular degeneration (AMD). It is now shown that the presence of high exogenous concentrations of all-trans-retinal in photoreceptor outer segments leads to the formation of A2-rhodopsin (A2-Rh), an unprecedented fluorescent rhodopsin adduct which consists of bisretinoids (A2) linked to each of three lysine residues in rhodopsin (Rh) and which exhibits an emission spectrum similar to A2E. The fluorophore to protein ratio was determined by MALDI-TOF-MS and UV-VIS spectroscopy. Enzymatic degradation with thermolysin and cathepsin D showed that two of the A2 moieties were located in the region of the third cytoplasmic loop and 8th helix of Rh. Examination of A2-Rh and A2-PE (the precursor of A2E) fluorescence in relation to all-trans-retinal concentration indicated that whereas A2-PE formation is favored over that of A2-Rh, for a single rhodopsin molecule only one phosphatidylethanolamine molecule is available to react with all-trans-retinal; this phosphatidylethanolamine is probably tightly associated with the protein.     

A New Interpretation of Apparent Induction Period in Ring‐Opening Polymerization of Octamethylcyclotetrasiloxane in Acid Emulsion

A following new interpretation of apparent induction period is proposed considering the experimental results obtained: octamethylcyclotetrasiloxane (D4) is activated by the reaction with acid to generate an activated derivative (A4). A4 reacts with D4 to generate A8, an active species containing eight dimethylsiloxane units. A8 backbites to generate mostly A4 and D4, which causes retardation in polymerization, but occasionally to form A3 and D5. A3 is highly reactive, and when the concentration of A3 exceeds a certain limit, much Ai where i is large enough is formed and promotes fast growth of chain at the interfacial area due to high concentration of D4. The interpretation assumes that A3 accelerates growth of chain faster than other species, and that A8 tends to backbite rather than grow. The interpretation is supported by the experimental results of polymerization conducted with D4 and D3, or D5 and D3 charged.     

Synthesis of lipid A derivatives and their interactions with polymyxin B and polymyxin B nonapeptide

Lipid A is the causative agent of Gram-negative sepsis, a leading cause of mortality among hospitalized patients. Compounds that bind lipid A can limit its detrimental effects. Polymyxin B, a cationic peptide antibiotic, is one of the simplest molecules capable of selectively binding lipid A and may serve as a model for further development of lipid A binding agents. However, association of polymyxin B with lipid A is not fully understood, primarily due to the low solubility of lipid A in water and inhomogeneity of lipid A preparations. To better understand lipid A-polymyxin B interaction, pure lipid A derivatives were prepared with incrementally varied lipid chain lengths. These compounds proved to be more soluble in water than lipid A, with higher aggregation concentrations. Isothermal titration calorimetric studies of these lipid A derivatives with polymyxin B and polymyxin B nonapeptide indicate that binding stoichiometries (peptide to lipid A derivative) are less than 1 and that affinities of these binding partners correlate with the aggregation states of the lipid A derivatives. These studies also suggest that cooperative ionic interactions dominate association of polymyxin B and polymyxin B nonapeptide with lipid A.     

Modulating the coupling efficiency of human cytochrome P450 CYP3A4 at electrode surfaces through protein engineering

This study shows that regulating the electron flow to the heme of human cytochrome P450 CYP3A4, using artificial redox chains, can significantly enhance its coupling efficiency and catalytic activity at electrode surfaces. The human CYP3A4 was fused at the genetic level either to the reductase domain of CYP102A1 (BMR) to create the CYP3A4/BMR or to Desulfovibrio vulgaris flavodoxin (FLD) to create the CYP3A4/FLD. Direct electrochemistry of the CYP3A4, CYP3A4/BMR and CYP3A4/FLD on glassy carbon and gold electrodes showed that the BMR and FLD flavo-proteins reduced the electron transfer rate to the CYP3A4 heme. Electrocatalysis resulted in appreciably higher product formation with the immobilized CYP3A4/BMR and CYP3A4/FLD on both surfaces due to an increased coupling efficiency. Rotating disk electrode studies and quantification of hydrogen peroxide were consistent with the proposed mechanism of a longer lived iron-peroxy species in the immobilized CYP3A4/BMR and CYP3A4/FLD. The approaches in this study provide a better understanding of cytochrome P450 uncoupling at electrode surfaces and aids in the construction of improved cytochrome P450 biosensors and bioelectrocatalysts.     

Immobilization of concanavalin A to glucose‐containing polymers

Sol‐gel reversible hydrogels sensitive to environmental glucose concentration were prepared using concanavalin A (Con A) and glucose‐containing polymers. Since the components of the hydrogels in the sol state can be released to the environment through pores of the dialysis membrane, it was necessary to immobilize Con A to the glucose‐containing polymers. Con A was immobilized by two different approaches. First, vinyl groups were introduced to Con A so that it can participate in the vinyl polymerization of allyl glucoside. Second, glucose‐containing polymers containing chemically reactive pendant groups were synthesized so that Con A could be immobilized to the preformed polymers. Both approaches resulted in effective immobilization of Con A to the glucose‐containing polymers, but the second method appeared to be better in terms of maintaining the bioactivity of Con A.     

Molecular modeling of A1 and A2A adenosine receptors: comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies

Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors. The homology models of adenosine A1 and A2A receptors were constructed. The high-resolution X-ray structure of bovine rhodopsin and crystal structure of beta2-adrenergic receptor were used as templates. The binding sites of the A1 and A2A ARs were constructed by using data obtained from mutagenesis experiments as well as docking simulations of the respective AR antagonsists DPCPX and XAC. To compare rhodopsin- and beta2-adrenergic-based models, the binding mode of A1 (KW-3902, LUF-5437) and A2A (KW-6002, ZM-241385) ARs antagonists were also examined. The differences in the binding ability of both models were noted during the study. The beta2-adrenergic-based A2A AR model was much more capable to stabilize the ligand in the binding site cavity than the corresponding rhodopsin-based A2A AR model, however, such differences were not so clear in case of A1 AR models. It was suggested that for the A1 AR it is possible to use the crystal structure of rhodopsin as a template as well as beta2-adrenergic receptor, but for A2A AR, with the now available beta2-adrenergic receptor X-ray structure, docking studies should be avoided on the rhodopsin-based model. However, taking into account that the beta2AR shares about 31% of the residues with the AR in comparison to 21% in case of bRho, we suggest using beta2-adrenergic-based models for the A1 and A2A ARs for further in silico ligand screening also because of their generally better ability to stabilize ligands inside the binding pocket.     

Synthesis of indole-based oxadiazoles and their interaction with bacterial peptidoglycan and SARS-CoV-2 main protease: In vitro,molecular docking and in silico ADME/Tox study

In the present study, Indole-based-oxadiazole (1A-17A) compounds were successfully synthesized. The structures of all synthesized compounds were fully characterized by different sophisticated spectroscopic techniques such 1H NMR, 13C NMR, and HREI-MS. Further, the synthesized compounds were explored to investigate their broad-spectrum antibacterial and antibiofilm potential against multidrug resistant Pseudomonas aeruginosa (MDR-PA) and methicillin resistant Staphylococcus aureus (MRSA). The compounds possessed a broad spectrum of antibacterial activity having MIC values of values 1–8 mg/ml against the tested microorganisms. Compound A6 and A7 shows maximum antibacterial activity against MDR-PA, whereas A6, A7 and A11 shows highest activity against MRSA. Furthermore, antibiofilm assay shows that A6, A7 and A11 showed maximum inhibition of biofilm formation and it was found that at 4 mg/ml; A6, A7 and A11 inhibit MRSA biofilm formation by 81.1, 77.5 and 75.9%, respectively; whereas in case of P. aeruginosa; A6 and A7 showed maximum biofilm inhibition and inhibit biofilm formation by 81.5 and 73.7%, respectively. Molecular docking study showed that compounds A6, A7, A8, A10, and A11 had high binding affinity to bacterial peptidoglycan, indicating their potential inhibitory activity against tested bacteria, whereas A6 and A11 were found to be the most effective inhibitors of SARS CoV-2 main protease (3CLpro), with a binding affinity of ? 7.78 kcal/mol. Furthermore, SwissADME and pkCSM-pharmacokinetics online tools was applied to calculate the ADME/Tox profile of the synthesized compounds and the toxicity of these chemicals was found to be low. The Lipinski, Veber, Ghose, and Consensus LogP criteria were also used to predict drug-likeness levels of the compounds. Our findings imply that the synthesized compounds could be a useful for the preventing and treating biofilm-related microbial infection as well as SARS-CoV2 infections.     

The HLA-A2-supermotif: a QSAR definition

Identification of epitopes capable of binding multiple HLA types will significantly rationalise the development of epitope-based vaccines. A quantitative method assessing the contribution of each amino acid at each position was applied to over 500 nonamer peptides binding to 5 MHC alleles--A*0201, A*0202, A*0203, A*0206 and A*6802--which together define the HLA-A2-like supertype. FXIGXI (L)IFV was identified as a supermotif for the A2-supertype based on the contributions of the common preferred amino acids at each of the nine positions. The results indicate that HLA-A*6802 is an intermediate allele standing between A2 and A3 supertypes: at anchor position 2 it is closer to A3 and at anchor position 9 it is nearer to A2. Models are available free on-line at http://www.jenner.ac.uk/MHCPred and can be used for binding affinity prediction.     

Recent research and development of DYRK1A inhibitors

Dual specificity tyrosine phosphorylation regulated kinase 1 A(DYRK1 A) is an evolutionarily conserved protein kinase belonging to the CMGC kinase family, which is closely related to Down syndrome(DS)and Alzheimer’s disease(AD). In recent years, not only the treatment of diabetes, but also the treatment of cancer gradually focuses on targeting DYRK1 A. Therefore, a series of DYRK1 A inhibitors have been developed to treat relevant diseases and clarify their treatment mechanism furtherly. DYRK1 A...     

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface.     

Simultaneous quantitation of Aspergillus flavus/A. parasiticus and aflatoxins in peanuts

A method was developed for simultaneous quantitation of Aspergillus flavus/A. parasiticus and aflatoxins in peanuts. Peanut samples were ground with an equal weight of water in a vertical cutter mixer to produce a slurry. Separate subsamples were taken for dilution-plating to determine total colony forming units (CFU)/g of A. flavus/A. parasiticus and for liquid chromatographic analysis to determine aflatoxin concentrations. Dry-grinding peanuts for homogenization of aflatoxins produced high temperatures that killed most of the A. flavus/A. parasiticus propagules. Addition of water to produce a slurry kept the temperature from rising above levels that killed the fungi. A 7 min grind time provided optimal homogenization for both the fungi and aflatoxins, so long as the temperature of the slurry did not exceed 45 degrees C. In the analysis of 60 shelled peanut samples, total aflatoxin concentrations ranged from 0 to 10,000 ng/g and total A. flavus/A. parasiticus ranged from 1.4 x 10(3) to 3.2 x 10(6) CFU/g. Regression analysis showed a significant positive correlation (p < 0.0001) between the quantities of A. flavus/A. parasiticus and aflatoxin (R2 = 0.82).     

Evaluation of the thermodynamic parameters for the adsorption of some hydrocarbons on alumina and molecular sieves 3A and 5A by inverse gas chromatography

Inverse gas chromatography has been used to evaluate the adsorption parameters (deltaH, deltaS and deltaG) of some probes, each representing a class of organic compounds (n-hexane, cyclohexane and benzene) on some adsorbents (activated alumina, and molecular sieves 3A and 5A). It was found that benzene exhibits more negative deltaH than for n-hexane and cyclohexane on molecular sieves 3A and 5A and alumina. Also, interactions of the benzene with molecular sieves 3A and 5A were found to be stronger than that on alumina. On the contrary, interactions of the hexane with alumina were found to be stronger than those on molecular sieves 3A and 5A.     

Modification of a Small β‐Barrel Protein,To Give Pseudo‐Amyloid Structures,Inhibits Amyloid β‐Peptide Aggregation

Aggregation of amyloid β‐peptide (Aβ) is closely related to the pathogenesis of Alzheimer’s disease (AD). Although much effort has been devoted to the construction of molecules that inhibit the aggregation of Aβ1‐42, high doses are needed for the inhibition of Aβ aggregation in many cases. Previously, we reported that designed green fluorescent protein (GFP) analogues that gives pseudo‐Aβ β‐sheet structures can work as an aggregation inhibitor against Aβ. To further test this design strategy, we constructed protein analogues that mimic Aβ β‐sheet structures of amyloids by using insulin‐like growth factor 2 receptor domain 11 (IGF2R‐d11) as a scaffold. A designed protein, named IG11KK, which has a parallel configuration of Aβ‐like β sheets, can bind more preferentially to oligomeric Aβ1‐42 than the monomer. Moreover, IG11KK suppressed the aggregation of Aβ1‐42 efficiently, even though lower concentrations of IG11KK than Aβ were used. The aggregation kinetics of Aβ in the presence of the designed proteins revealed that IG11KK can work as an inhibitor not only for the early to middle stages, but also in the latter stage of Aβ aggregation owing to its favorable binding to oligomeric structures of Aβ. The design strategy using β‐barrel proteins such as IGF2R‐d11 and GFP is useful in generating excellent inhibitors of protein misfolding and amyloid formation.     

Molecularly asymmetric triblock copolymers as a single-molecule route to ordered bidisperse polymer brushes

The conditions signaling the formation of bidisperse brushes in ordered block copolymers are investigated as an A(2) block is progressively grown onto an A(1)B diblock copolymer to form a series of molecularly asymmetric, isomorphic A(1)BA(2) triblock copolymers. Small-angle scattering and self-consistent field theory confirm that the microphase-ordered period decreases when the A(2) block is short relative to the A(1) block, but then increases as A(1)+A(2) bidisperse brushes develop. The mechanical properties systematically follow the spatial distribution of the A(2) block.