Characterization of PDZ domain–peptide interactions using an integrated protocol of QM/MM,PB/SA,and CFEA analyses

Protein–protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains. Characterizing the interaction interface of domain–peptide complexes and analyzing binding specificity for modular domains are critical for deciphering protein–protein interaction networks. In this article, we report the successful use of an integrated computational protocol to dissect the energetic profile and structural basis of peptide binding to third PDZ domain (PDZ3) from the PSD-95 protein. This protocol employs rigorous quantum mechanics/molecular mechanics (QM/MM), semi-empirical Poisson–Boltzmann/surface area (PB/SA), and empirical conformational free energy analysis (CFEA) to quantitatively describe and decompose systematic energy changes arising from, respectively, noncovalent interaction, desolvation effect, and conformational entropy loss associated with the formation of 30 affinity-known PDZ3–peptide complexes. We show that the QM/MM-, PB/SA-, and CFEA-derived energy components can work together fairly well in reproducing experimentally measured affinity after a linearly weighting treatment, albeit they are not compatible with each other directly. We also demonstrate that: (1) noncovalent interaction and desolvation effect donate, respectively, stability and specificity to complex architecture, while entropy loss contributes modestly to binding; (2) P₀ and P₋₂ of peptide ligand are the most important positions for determining both the stability and specificity of the PDZ3–peptide complex, P₋₁ and P₋₃ can confer substantial stability (but not specificity) for the complex, and N-terminal P₋₄ and P₋₅ have only a very limited effect on binding.     

Peptide separation through a CB[8]-mediated supramolecular trap-and-release process

We demonstrate a supramolecular peptide separation approach by the selective immobilization of peptides bearing an N-terminal tryptophan onto a CB[8]-modified gold substrate, followed by electrochemical release. The CB[8]-stabilized heteroternary complexes were characterized by (1)H NMR, ESI-MS, UV/vis, and fluorescence spectroscopy and cyclic voltammetry. Micropatterned CB[8]-modified gold substrates were found to trap only the recognizable N-tryptophan-containing peptides from a peptide mixture that could be visualized as green peptide arrays under fluorescence microscopy. Subsequently, the bound peptides were released from the modified substrates by the controlled single-electron reduction of viologen. The fully reversible trap-and-release process was repeated for 13 cycles, and the cumulative release profile of the dye-peptide conjugate was monitored by fluorescence spectroscopy, indicating that no degradation occurred.     

Cell adhesive and growth behavior on electrospun nanofibrous scaffolds by designed multifunctional composites

Nanostructured biocomposite scaffolds of poly(l-lactide) (PLLA) blended with collagen (coll) or hydroxyapatite (HA), or both for tissue engineering application, were fabricated by electrospinning. The electrospun scaffolds were characterized for the morphology, chemical and tensile properties by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), water contact angle (WCA), Fourier transform infrared (FTIR) measurement, and tensile testing. Electrospun biocomposite scaffolds of PLLA and collagen or (and) HA in the diameter range of 200-700 nm mimic the nanoscale structure of the extracellular matrix (ECM) with a well-interconnection pore network structure. The presence of collagen in the scaffolds increased their hydrophility, and enhanced cell attachment and proliferation, while HA improved the tensile properties of the scaffolds. The biocompatibility of the electrospun scaffolds and the viability of contacting cells were evaluated by 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) nuclear staining and by fluorescein diacetate (FDA) and propidium iodide (PI) double staining methods. The results support the conclusion that 293T cells grew well on composite scaffolds. Compared with pure PLLA scaffolds a greater density of viable cells was seen on the composites, especially the PLLA/HA/collagen scaffolds.     

One-pot and microwave-assisted synthesis of N-sulfonylaziridines

A novel and efficient microwave-assisted one-step reaction was developed to synthesize chiral N-sulfonylaziridines by the reaction of different chiral amino alcohols and sulfonic chlorides. The newly developed microwave synthetic method has the advantage of reducing the reaction time from 24 to 0.5 h with improved yields (84-93%) and minimizing by-products.     

Coal pyrolysis in a fluidized bed reactor simulating the process conditions of coal topping in CFB boiler

Simulating the conditions of pyrolytic topping in a fluidized bed reactor integrated into a CFB boiler, the study was devoted to the reaction fundamentals of coal pyrolysis in terms of the production characteristics of pyrolysis oil in fluidized bed reactors, including pyrolysis oil yield, required reaction time and the chemical species presented in the pyrolysis oil. The results demonstrated that the maximal pyrolysis oil yield occurred on conditions of 873 K, with a reaction time of 3 min and in a reaction atmosphere gas simulating the composition of pyrolysis gas. Adding H₂ and CO₂ into the reaction atmosphere decreased the pyrolysis oil yield, while the oil yield increased with increasing the CO and CH₄ contents in the atmosphere. TG-FTIR analysis was conducted to reveal the effects of reaction atmosphere on the chemical species present in the pyrolysis oil. The results clarified that the pyrolysis oil yield reached its maximum when the simulated pyrolysis gas was the reaction atmosphere, but there were slightly fewer volatile matters in the pyrolysis oil than the oil generated in the N₂ atmosphere. All of these results are expected not only to reveal the composition characteristics of the pyrolysis oil from different conditions of the coal topping process but also to optimize the pyrolysis conditions in terms of maximizing the light pyrolysis oil yield and quality.     

Preparation and drug release behavior of temperature-responsive mesoporous carbons

A temperature-responsive composite based on poly (N-isopropylacrylamide) (PNIPAAm) and ordered mesoporous carbons (OMCs) has been successfully prepared by a simple wetness impregnation technique. The structures and properties of the composite were characterized by infrared spectroscopy (IR), X-ray diffraction (XRD), transmission electron microscopy (TEM), N₂ sorption, thermogravimetric analysis (TG) and differential scanning calorimetry (DSC). The results showed that the inclusion of PNIPAAm had not greatly changed the basic ordered pore structure of the OMCs. Ibuprofen (IBU) was selected as model drug, and in vitro test of IBU release exhibited a temperature-responsive controlled release delivery.     

Selective solid-phase extraction and separation of trace gold, palladium and platinum using activated carbon modified with ethyl-3-(2-aminoethylamino)-2-chlorobut-2-enoate

Activated carbon was chemically modified with ethyl-3-(2-aminoethylamino)-2-chlorobut-2-enoate to obtain a material for selective solid-phase extraction of trace Au(III), Pd(II) and Pt(IV) prior to their determination by inductively coupled plasma atomic emission spectrometry. Experimental conditions such as effects of pH, shaking time, sample flow rate and volume, elution and interfering ions were studied. The ions Au(III), Pd(II) and Pt(IV) can be quantitatively adsorbed on the new sorbent from solution of pH 1. The adsorbed ions were then eluted with 0.1 mol L^?1 hydrochloric acid and containing 4% thiourea. Many common ions do not interfere. The adsorption capacity of the material is 305, 92, and 126 mg g^?1 for Au(III), Pd(II) and Pt(IV), respectively, and the detection limits are 5, 11 and 9 ng mL^?1. The relative standard deviation is less than 3.0% (n?=?8) under optimum conditions. The method was validated by analyzing two certified reference materials and successfully applied to the preconcentration and determination of these ions in actual samples with satisfactory results.

4-氨基-N8,N10-二碳杂-N5-取代四氢叶酸类似物的合成及生物活性研究

以2,4-二氨基-6-羟甲基吡啶并[3,2-d]嘧啶为原料,与对甲酰基苯甲酰谷氨酸二乙酯发生Wittig反应构建叶酸类似物的骨架结构,还原吡啶环得到4-氨基-8,10-二碳杂四氢叶酸类似物,在N5位取代不同基团得到四个新的4-氨基-N8,N10-二碳杂四氢叶酸类化合物,经1H NMR,13C NMR和MS对化合物的结构进行了表征.初步生物活性结果表明,此类化合物对人重组胸苷酸合成酶的抑制作用与N5位取代基有关,2个化合物在0.1 μmol·L-1的浓度下对HL-60白血病细胞的抑制率达到60％以上.     

Optimization of a Multiplex PCR Assay for Detecting Transgenic Soybean Components in Feed Products

A multiplex polymerase chain reaction (m-PCR) assay was developed for the simultaneous detection of multiple components of genetically modified (GM) soybean. It uses two sets of primers (I, lectin1/35S/CP4; II, lectin2/35S/CP4) specific for a soybean reference gene, the 35S promoter, and an event-specific gene. Amplified fragments of 118, 414, 195, and 320 bp were easily detected by agarose gel electrophoresis and were positively confirmed by sequencing. Primer set concentrations and annealing temperatures in the m-PCR were optimized. The optimized m-PCR conditions were obtained for primer set I at a ratio of 1:2:3 and a 59.2 °C annealing temperature and set II at the same ratio and 58.6 °C, 60.3 °C, and 61.2 °C annealing temperatures. The sensitivities of the two m-PCR primer sets (I and II) were 0.25% and 0.5%, respectively. The results showed that this m-PCR assay provides rapid, reliable, and effective identification of multiple components of GM soybean in feed.     

Co-overexpression of PpPDI Enhances Secretion of Ancrod in Pichia pastoris

Ancrod, a serine protease purified from the venom of Agkistrodon rhodostoma, is highly specific for fibrinogen. It causes anticoagulation by defibrinogenation and has been used as a therapeutic anticoagulant for the treatment of moderate to severe forms of peripheral arterial circulatory disorders in a variety of countries. The DNA of ancrod was amplified by recursive PCR with a yeast bias codon and cloned into the pGEM-T Easy vector. In order to achieve a high level secretion and a full activity expression of ancrod in Pichia pastoris (P. pastoris), the P. pastoris protein disulfide bond isomerase (PpPDI) was co-overexpressed in the strain. The secretion characteristics of ancrod with and without PpPDI were examined. With co-overexpression of PpPDI, the production of recombinant ancrod (rAncrod) was increased to 315 mg/L in the culture medium, which is twofold higher than the control strain carrying only the ancrod gene. Through purified by Ni2? affinity chromatography and phenyl Sepharose column, the purity of rAncrod was found to be as high as 95.2%. The fibrinogenolytic and zymographic activities of the rAncrod were determined and found to be similar to that of the native protein. This improved expression system can facilitate further studies and the industrial production of ancrod.