The synthesis and modification of highly fluorescent carbon quantum dots for reversible detection of water‐soluble phosphonate‐1‐hydroxyethane‐1,1‐diphosphonic acid by fluorescence spectroscopy

Photoluminescent (PL) carbon quantum dots (CQDs) were prepared successfully using a facile and green procedure. They exhibited striking blue fluorescence and excellent optical properties, with a quantum yield as high as 61.44%. Due to the fluorescence quenching effect and the stronger complexing ability of the phosphoric acid group of 1‐hydroxyethane‐1,1‐diphosphonic acid (HEDP) to Fe³⁺ , CQDs doped with Fe³⁺ were adequately constructed as an efficient and sensitive fluorescent probe for HEDP‐specific sensing. The proposed fluorescent probe had a sensitive and rapid response in the range 5–70 μ M. Furthermore, quantitative molecular surface (QMS) analysis based on the Multiwfn program was applied to explore the complexation mode of HEDP and metal ions. The distribution of electrostatic potential (ESP), average local ionization energy (ALIE), the minimum value points and the position of the lone pair electrons on the surface of molecular van der Waals were further determined. More strikingly, this experiment achieved the quantitative detection of water‐soluble phosphonate‐HEDP, for the first time using fluorescence spectrometry. It has been proved to be an effective and intuitive sensing method for the detection of HEDP in real samples.     

Predicting binding modes of reversible peptide‐based inhibitors of falcipain‐2 consistent with structure–activity relationships

Falcipain‐2 (FP‐2) is a major hemoglobinase of Plasmodium falciparum, considered an important drug target for the development of antimalarials. A previous study reported a novel series of 20 reversible peptide‐based inhibitors of FP‐2. However, the lack of tridimensional structures of the complexes hinders further optimization strategies to enhance the inhibitory activity of the compounds. Here we report the prediction of the binding modes of the aforementioned inhibitors to FP‐2. A computational approach combining previous knowledge on the determinants of binding to the enzyme, docking, and postdocking refinement steps, is employed. The latter steps comprise molecular dynamics simulations and free energy calculations. Remarkably, this approach leads to the identification of near‐native ligand conformations when applied to a validation set of protein‐ligand structures. Overall, we proposed substrate‐like binding modes of the studied compounds fulfilling the structural requirements for FP‐2 binding and yielding free energy values that correlated well with the experimental data. Proteins 2017; 85:1666–1683. © 2017 Wiley Periodicals, Inc.     

Preparation and application of solvent‐modulated self‐doped N–S multicolour fluorescence carbon quantum dots

In this paper, two types of carbon quantum dot (CQDs) were prepared using biocompatible l ‐methionine as the carbon source and urea as the nitrogen source and a one‐step hydrothermal treatment. By changing the reaction solvents (deionized (DI) water and dimethylformamide (DMF)), the maximum emission of the resulting CQDs shifted from blue to red light. Specifically, the emission wavelength of the CQDs moved from 433 nm to 625 nm following embedding of a new functional group (–CONH–) on the surface of the CQDs. Photoluminescence quantum yields of the CQDs with blue and red emission reached 64% and 61%, respectively. The R‐CQDs were used to detect metal ions and a linear relationship was demonstrated between ln(F/F₀) and Fe³⁺ concentration in the range 0–0.5 mmol/L with a detection limit of 0.067 μM. Therefore these R‐CQDs have great potential as fluorescent probes for Fe³⁺ detection. We expect that the excellent water‐soluble, biocompatible and optical properties of the CQDs developed in this work mean that they will be widely used to detect biological cells.     

Highly sensitive spectrofluorimetic determination of rutin based on its activated effect on a multi‐enzyme redox system

A highly sensitive and simple spectrofluorimetric method for the determination of rutin, based on its activated effect on a haemoglobin‐catalysed reaction, was developed. Under optimum conditions, the concentration of rutin was linear, with decreased fluorescence (ΔF) of the system under optimal experimental conditions. The calibration graph was linear in the range 1.0 × 10^–7–3.0 × 10^–5 mol/L, with a detection limit of 7.0 × 10^–8 mol/L. The relative standard deviation (RSD) was 3.26% for 11 determinations of 1.0 × 10^–5 mol/L. This method was used for the determination of rutin in pharmaceuticals with satisfactory results. Copyright © 2011 John Wiley & Sons, Ltd.     

Spectroscopic analysis on structure–affinity relationship in the interactions of different oleanane‐type triterpenoids with bovine serum albumin

Oleanane‐type triterpenoids serve as an important group of plant secondary metabolites with a variety of biological activities and the C‐3 position substitution pattern is a significant structural feature for their biological activities. Three selected oleanane‐type triterpenoids (glycyrrhizin, glycyrrhetinic acid, and carbenoxolone) bearing different substituents (glucuronic acid dimer, hydroxyl, and succinyl groups) at the C‐3 position were studied for their affinities to bind bovine serum albumin (BSA) by steady‐state fluorescence, synchronous, three‐dimensional fluorescence and ultraviolet–visible (UV–vis) absorption spectra. The binding mechanism of the triterpenoids to BSA is due to the formation of the triterpenoids–BSA complex and the binding affinity is strongest for carbenoxolone and ranked in the order carbenoxolone > glycyrrhetinic acid > glycyrrhizin. The thermodynamic parameters calculated at different temperatures showed that triterpenoids binding to BSA primarily depended on hydrophobic interaction and hydrogen bonding. The distance between the bound triterpenoid and BSA was determined on the basis of the Förster's energy transfer theory. Displacement experiments using phenylbutazone and ibuprofen showed the binding site of triterpenoids on BSA at subdomain IIA (Sudlow's site I). The effect of triterpenoids on BSA conformation was analyzed by UV–vis absorption, and synchronous and three‐dimensional fluorescence spectra. These results revealed that the C‐3 position substitution pattern significantly affects the structure–affinity relationships of oleanane‐type triterpenoid binding to BSA and further affects the bioavailability of triterpenoids in the blood circulatory system. Copyright © 2014 John Wiley & Sons, Ltd.     

Receptor assay guided structure‐activity studies of helicokinin insect neuropeptides and peptidomimetic analogues

Neuropeptides control numerous physiological processes in insects. The regulation of water balance is a crucial aspect of homeostasis in terrestrial insects and has been shown to be under endocrine control, primarily by corticotrophin releasing factor (CRF)‐related peptides and kinins. For helicokinin I, a diuretic neuropeptide from the economically important insect pest Heliothis virescens, detailed structure‐activity relationships have been established based on truncated structures, diverse amino acid scans and peptidomimetic analogues. The activities of selected compounds on functional expressed helicokinin receptors are compared with the results of a Malphigian tubule assay. Implications for further peptidomimetic variations are provided. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

A multiscale approach to simulating the conformational properties of unbound multi‐C2H2 zinc finger proteins

The conformational properties of unbound multi‐Cys₂His₂ (mC₂H₂) zinc finger proteins, in which zinc finger domains are connected by flexible linkers, are studied by a multiscale approach. Three methods on different length scales are utilized. First, atomic detail molecular dynamics simulations of one zinc finger and its adjacent flexible linker confirmed that the zinc finger is more rigid than the flexible linker. Second, the end‐to‐end distance distributions of mC₂H₂ zinc finger proteins are computed using an efficient atomistic pivoting algorithm, which only takes excluded volume interactions into consideration. The end‐to‐end distance distribution gradually changes its profile, from left‐tailed to right‐tailed, as the number of zinc fingers increases. This is explained by using a worm‐like chain model. For proteins of a few zinc fingers, an effective bending constraint favors an extended conformation. Only for proteins containing more than nine zinc fingers, is a somewhat compacted conformation preferred. Third, a mesoscale model is modified to study both the local and the global conformational properties of multi‐C₂H₂ zinc finger proteins. Simulations of the CCCTC‐binding factor (CTCF), an important mC₂H₂ zinc finger protein for genome spatial organization, are presented. Proteins 2015; 83:1604–1615. © 2015 Wiley Periodicals, Inc.     

Conformational and aggregation properties of the 1–93 fragment of apolipoprotein A‐I

Several disease‐linked mutations of apolipoprotein A‐I, the major protein in high‐density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N‐terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril‐associated disordered 1–93 fragment of this protein, in wild‐type and mutated (G26R, S36A, K40L, W50R) forms. In atomic‐level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position‐dependent β‐strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease‐linked aggregation of apolipoprotein A‐I.     

Review: An overview about the structure–function relationship of marine sulfated homopolysaccharides with regular chemical structures

Efforts in both structural and biological studies of sulfated polysaccharides from marine organisms have increased significantly over the last 10 years. Marine invertebrates have been demonstrated to be a source of glycans with particularly well‐defined chemical structures, although ordered structural patterns can also be found occasionally in algal sources such as red seaweeds. Clear and regular structural features are essential for a good understanding of the biological activities of these marine homopolysaccharides of which sulfated fucans and sulfated galactans are the most studied. Herein, the main structural features (sugar type, sulfation and glycosylation sites, and orientational binding preferences) of both sulfated fucans and galactans are individually reviewed with regard to their specific contributions to two frequently described biological functions: the acrosome reaction (a physiological event of sea‐urchin fertilization), and the anticoagulant and antithrombotic activities (an alternative and highly desirable pharmacological application). © 2009 Wiley Periodicals, Inc. Biopolymers 91: 601–609, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Synthesis,crystal structure and fluorescence properties of terbium complexes with phenoxyacetic acid and 2,4,6‐tris‐(2‐pyridyl)‐s–triazine

Two complexes of Tb³⁺, Gd³⁺/Tb³⁺ and one heteronuclear crystal Gd³⁺/Tb³⁺ with phenoxyacetic acid (HPOA) and 2,4,6‐tris‐(2‐pyridyl)‐s–triazine (TPTZ) have been synthesized. Elemental analysis, rare earth coordination titration, inductively coupled plasma atomic emission spectrometry (ICP‐AES) and thermogravimetric analysis‐differential scanning calorimetry (TG‐DSC) analysis show that the two complexes are Tb₂(POA)₆(TPTZ)₂·6H₂O and TbGd(POA)₆(TPTZ)₂·6H₂O, respectively. The crystal structure of TbGd(POA)₆(TPTZ)₂·2CH₃OH was determined using single‐crystal X‐ray diffraction. The monocrystal belongs to the triclinic system with the P‐1 space group. In particular, each metal ion is coordinately bonded to three nitrogen atoms of one TPTZ and seven oxygen atoms of three phenoxyacetic ions. Furthermore, there exist two coordinate forms between C₆H₅OCH₂COO^– and the metal ions in the crystal. One is a chelating bidentate, the other is chelating and bridge coordinating. Fluorescence determination shows that the two complexes possess strong fluorescence emissions. Furthermore, the fluorescence intensity of the Gd³⁺/Tb³⁺ complex is much stronger than that of the undoped complex, which may result from a decrease in the concentration quench of Tb³⁺ ions, and intramolecular energy transfer from the ligands coordinated with Gd³⁺ ions to Tb³⁺ ions. Copyright © 2015 John Wiley & Sons, Ltd.     

Structure–activity relationship study of antioxidative peptides by QSAR modeling: the amino acid next to C‐terminus affects the activity

Screening, isolation and in vitro assays have been used for characterization of antioxidative peptides derived from food proteins, and incompatible deductions of structural characteristics derived from the isolated peptides have been brought forward. However, there is still little information concerning the structure‐activity relationship of antioxidative peptides. QSAR modeling was performed, respectively, on synthetic tripeptides and tetrapeptides related to LLPHH. According to cumulative squared multiple correlation coefficients (R²), cumulative cross‐validation coefficients (Q²) and relative standard deviation for calibration set (RSD_c), two credible models for tripeptide and tetrapeptide databases, respectively, have been built with partial least squares (PLS) regression (R² for models of tripeptide and tetrapeptide are 0.744 and 0.943, Q² are 0.631 and 0.414, and RSD_c are 0.323 and 0.111, respectively). Meanwhile, according to the cumulative multiple correlation coefficient for the predictive set ($R_{\rm {ext}}^{2}$ ) and the relative standard deviation for the predictive set (RSD_p), the predictive ability of the model for tripeptides also is excellent ($R_{\rm {ext}}^{2}$ and RSD_p are 0.719 and 0.450, respectively). Hydrogen bond property and hydrophilicity of the amino acid residue next to the C‐terminus, and the hydrophobicity as well as electronic propertyof the N‐terminus are more significant; meanwhile, the electronic property of the C‐terminus is beneficial for antioxidant activity. The structural characteristics we found are very useful in understanding and predicting the peptide structures responsible for activity and development of functional foods with peptides as active compounds, or antioxidative peptides as alternatives to other antioxidants. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Application of quantitative structure‐activity relationship analysis on an antibody and alternariol‐like compounds interaction study

The antigen‐antibody interaction determines the sensitivity and specificity of competitive immunoassay for hapten detection. In this paper, the specificity of a monoclonal antibody against alternariol‐like compounds was evaluated through indirect competitive ELISA. The results showed that the antibody had cross‐reactivity with 33 compounds with the binding affinity (expressed by IC₅₀) ranging from 9.4 ng/mL to 12.0 μg/mL. All the 33 compounds contained a common moiety and similar substituents. To understand how this common moiety and substituents affected the recognition ability of the antibody, a three‐dimensional quantitative structure‐activity relationship (3D‐QSAR) between the antibody and the 33 alternariol‐like compounds was constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The q² values of the CoMFA and CoMSIA models were 0.785 and 0.782, respectively, and the r² values were 0.911 and 0.988, respectively, indicating that the models had good predictive ability. The results of 3D‐QSAR showed that the most important factor affecting antibody recognition was the hydrogen bond mainly formed by the hydroxyl group of alternariol, followed by the hydrophobic force mainly formed by the methyl group. This study provides a reference for the design of new hapten and the mechanisms for antibody recognition.     

Synthesis and properties of blue luminescent bipolar materials constructed with carbazole and anthracene units with 4‐cyanophenyl substitute at the 9‐position of the carbazole unit

With carbazole and p‐cyanobromobenzene as raw materials, 4‐(3,6‐di (anthracen‐9‐yl)‐9H‐carbazol‐9‐yl)benzonitrile (DACB) and 4‐(3,6‐bis(anthracene ‐9‐ylethynyl)‐9H‐carbazol‐9‐yl)benzonitrile (BACB) were synthesized through the Suzuki coupling reaction and the Sonogashira coupling reaction, respectively. These structures were characterized using ¹H nuclear magnetic resonance (NMR), elemental analysis and mass spectrometry. Their thermal properties, ultraviolet–visible (UV‐vis) absorption, fluorescence emission, fluorescence quantum yields and electrochemical properties were also investigated systematically. In addition, a electroluminescence (EL) device was made with BACB as the emitting layer and performance of the EL device was studied. Results showed that: (1) the temperature points with 5% and 10% of DACB weight loss were 443°C and 461°C, respectively, and were 475°C and 506°C with BACB weight loss of 5% and 10%, respectively. When the temperature was 50?300°C, no significantly thermal transition was observed which suggested that they had excellent thermal stability. (2) DACB and BACB had single emission peaks at 415 nm, and 479 nm with fluorescence quantum yields of 0.61 and 0.87, respectively, indicating that both compounds could emit strong blue light. (3) According to electrochemical measurement on BACB and DACB, their gaps were 3.07 eV and 2.76 eV, respectively, which further showed that these two compounds were very stable and acted as efficient blue light materials. (4) The turn‐on voltage of the device was 5 V, and the device emitted dark blue light with Commission Internationale de L'Eclairage (CIE) coordinates of (0.157, 0.079).     

Oxidative folding and preparation of α‐conotoxins for use in high‐throughput structure–activity relationship studies

α‐Conotoxins are peptide neurotoxins that selectively inhibit various subtypes of nicotinic acetylcholine receptors. They are important research tools for studying numerous pharmacological disorders, with profound potential for developing drug leads for treating pain, tobacco addiction, and other conditions. They are characterized by the presence of two disulfide bonds connected in a globular arrangement, which stabilizes a bioactive helical conformation. Despite extensive structure–activity relationship studies that have produced α‐conotoxin analogs with increased potency and selectivity towards specific nicotinic acetylcholine receptor subtypes, the efficient production of diversity‐oriented α‐conotoxin combinatorial libraries has been limited by inefficient folding and purification procedures. We have investigated the optimized conditions for the reliable folding of α‐conotoxins using simplified oxidation procedures for use in the accelerated production of synthetic combinatorial libraries of α‐conotoxins. To this end, the effect of co‐solvent, redox reagents, pH, and temperature on the proportion of disulfide bond isomers was determined for α‐conotoxins exhibiting commonly known Cys loop spacing frameworks. In addition, we have developed high‐throughput ‘semi‐purification’ methods for the quick and efficient parallel preparation of α‐conotoxin libraries for use in accelerated structure–activity relationship studies. Our simplified procedures represent an effective strategy for the preparation of large arrays of correctly folded α‐conotoxin analogs and permit the rapid identification of active hits directly from high‐throughput pharmacological screening assays. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Probing the interaction of l‐captopril with metallo‐β‐lactamase CcrA by fluorescence spectra and molecular dynamic simulation

Both the molecular recognition and interaction of metallo‐β‐lactamase CcrA with l ‐captopril were studied by the combined use of fluorescence spectra and molecular dynamic simulation. The results showed that the binding constant was 8.89 × 10⁴ L mol^?1 at 296 K. Both Zn1 and Zn2 displayed tetrahedral coordination geometries in the CcrA–Lcap complex, the S atom in l ‐captopril displaced the nucleophilic hydroxide in apo CcrA and occupied the fourth coordination site for each ion, resulting in a competitively inhibited CcrA enzyme. Strong electrostatic interaction between the two zinc ions in CcrA and negatively charged l ‐captopril provided the main driving force for the binding affinity. Through a partly structural transformation from β‐sheet to random coil, loop 1 (residues 24–34) completely opened the binding pocket of CcrA to allow an induced fit of the newly introduced ligand. This study may provide some valuable information for designing and developing a more tightly binding inhibitor to resist superbugs.     

The fourth level of social structure in a multi‐level society: ecological and social functions of clans in hamadryas baboons

Hamadryas baboons are known for their complex, multi‐level social structure consisting of troops, bands, and one‐male units (OMUs) [Kummer, 1968. Social organization of hamadryas baboons. Chicago: The University of Chicago Press. 189p]. Abegglen [1984. On socialization in hamadryas baboons: a field study. Lewisburg, PA: Bucknell University Press. 207p.] observed a fourth level of social structure comprising several OMUs that rested near one another on sleeping cliffs, traveled most closely together during daily foraging, and sometimes traveled as subgroups independently from the rest of the band. Abegglen called these associations “clans” and suggested that they consisted of related males. Here we confirm the existence of clans in a second wild hamadryas population, a band of about 200 baboons at the Filoha site in lowland Ethiopia. During all‐day follows from December 1997 through September 1998 and March 2005 through February 2006, data were collected on activity patterns, social interactions, nearest neighbors, band fissions, and takeovers. Association indices were computed for each dyad of leader males, and results of cluster analyses indicated that in each of the two observation periods this band comprised two large clans ranging in size from 7 to 13 OMUs. All band fissions occurred along clan lines, and most takeovers involved the transfer of females within the same clan. Our results support the notion that clans provide an additional level of flexibility to deal with the sparse distribution of resources in hamadryas habitats. The large clan sizes at Filoha may simply be the largest size that the band can split into and still obtain enough food during periods of food scarcity. Our results also suggest that both male and female relationships play a role in the social cohesion of clans and that males exchange females within clans but not between them. Am. J. Primatol. 71:948–955, 2009. © 2009 Wiley‐Liss, Inc.