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AbstractThe β42amyloid peptides (Aβ) are identified as a candidate target for Alzheimer’s drugs. Phenolic compounds can bind to the Aβ and inhibit amyloid formation. However, the inhibitory mechanism of phenolic compounds remains unclear. In this study, the molecular dynamic simulation and docking program were used to characterize the molecular details of inhibitory mechanism of the phenolic compounds. Our Results show that the phenolic compounds can bind to hydrophobic region in Aβ42monomer and alter hydrophobic interactions network at Aβ42which play a key role in β-sheet formation. The cluster analysis and interactions network analysis were used to probe conformational changes in Aβ42. In most populated clusters of Aβ42-phenolic compounds complexes, the sheet structures were not observed or reduced. It seems that the binding of phenolic compounds can induce larger conformational diversity for amyloid peptide and changes conformational properties of amyloid peptide. The phenolic compounds can deform β-Hairpin structure of Aβ by destabilizing salt bridges E22-K28 and D23-K28 which can alter the conformation of Aβ42in aqueoussolution. These findings are in accordance with experimental results, to some extent give a molecular level interpretation for the inhibitory mechanism of phenolic compounds .In addition, this study may add important new details to the inhibitory mechanism of Alzheimer’s drug.Communicated by Ramaswamy H. Sarma

•HRSEM and AFM confirmed the FTO surface has been modified as a robust biosensor.•By surfactant/stabilizer-free gold nanostructures on the FTO electrodes, is able to sense ultra-low level of microRNAs.•Our gold nanostructure surface is able to detect miR-9 at zepto molar level by electrochemistry approach.

In a total-internal-reflection-fluorescence-microscopy method, there is anisotropy in the polarized evanescent wave. Since the evanescent wave is used as an excitation field, the mentioned anisotropy is a disadvantage in using the total-internal-reflection-fluorescence-microscopy technique. Therefore, by theoretical and analytical approaches, and based on the Fresnel coefficients, the effect of three dielectrics media on the anisotropy of the evanescent wave is investigated. Following that, a proper combination of the cover glass, oil immersion, and prism for both living and non-living samples is suggested that not only enhances the intensity of the evanescent wave, but also and importantly, decreases the essential anisotropy of the evanescent wave.

AbstractSelf-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering.AbbreviationsMDMolecular DynamicsNSCsNeural Stem CellsPMEParticle mesh EwaldRDFRadial Distribution FunctionRGRadius of gyrationRASARelative Accessible Surface AreaRMSDRoot Mean Square DeviationsSASASolvent Accessible Surface Area.Communicated by Ramaswamy H. Sarma

In order to treat inflammatory bowel disease (IBD), there is an attempt to develop local drug delivery systems. The use of bioactive compounds such as gallic acid (GA) in a precise colon-targeting drug delivery platform is expected to enhance its bioavailability and increase local therapeutic responses. In this study, a novel cerasome-forming lipid (CFL) containing organosilane-based oleic acid was mixed with 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine via one-step construction to prepare composite cerasomes by varying mole ratios. The physicochemical properties, drug-loading capacity, long-term storage stability, and release rates of (GA) from cerasomes have been investigated. The size of cerasomal gallic acid (CG) was about 319 nm with −23 mV surface charge and 77% drug sustained released after 140 h in the simulated gastrointestinal fluids. Composite vesicles consisting of DPPC and CFL with a 1:1 M ratio exhibited good cytocompatibility and cellular uptake, also, the released gallic acid effectively inhibit the reactive species in LPS-induced inflammation of Caco-2 cells, compared to free (GA). Our results indicate that this novel CG has great potential to be applied as a non-ulcerogenic agent due to the prolonging duration of action in IBD therapy.

•Graphene oxide nano-wall decorated with gold nano-flower shape nanoparticle fabricated on the FTO surfaces.•The brucellosis outer membrane protein is immobilized on a fabricated nanostructure as a capture probe to detect the brucellosis antibodies.•The biosensor has a strong ability to detect brucellosis antibodies even in human serum.•Excellent specificity of the biosensor to distinguish brucellosis antibodies from non-specific targets was achieved.

MicroRNAs in serum/plasma have been introduced as novel, reliable and specific biomarkers for the detection, status monitoring and population screening of a disease. Along with molecular biology techniques, electrochemical biosensors have become the major biosensing method for miRNA quantification. Here we have tried to develop an electrochemical biosensing system which is simple, easy to prepare, highly sensitive and selective, cost-effective and has no need for sample preparation and/or amplification. We have evaluated an anthraquinone compound, Oracet Blue (OB), as an intercalative electroactive label for miRNA electrochemical biosensing. The proposed electrochemical biosensor was made of a thiolated single strand capture probe (SH-modified SS-probe) on an Au electrode (AuE). The role of OB was electrochemical signal transduction upon hybridization of the SS-probe to the target miRNA. Under optimized conditions, target miRNAs can be detected from 50 pM to 15 nM with a detection limit of 13.5 pM. The biosensor clearly discriminated the target miRNA from a single base mismatch and non-complementary target oligonucleotides, which could guarantee a high selectivity and specificity. Moreover, the results of the real sample assay of the proposed biosensor in human serum showed a good recovery percentage as well as high reproducibility which is promising for its future potential use in clinical applications.

Gonadotropin releasing hormone (GnRH) has a pivotal role in the biology of reproduction processes. In extrapituitary compartments GnRH and its receptor act as a part of the autocrin regulatory system of cell proliferation, resulting in its anticancer activity. Here the anticancer activity of a new analogue of GnRH has been investigated. Results indicate that proliferation of human breast and ovarian cancer cell lines is dose-dependently inhibited. The inhibitory efficiency of this new analogue is proved to be higher than the original triptorelin. In addition to its antimitogenic activity, evidence was found for the involvement of the apoptotic mechanism in the action of the new analogue. Furthermore the presence of chemical groups in the peptide sequence is thought to increase the protease stability of the new analogue in comparison with triptorelin. Consequently our new analogue can be considered as a good pharmaceutical candidate. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94: 292–297, 2010.

MicroRNAs (miRs) as biomarkers for early cancer diagnostic, were detected through a developed ultrasensitive electrochemical biosensor containing gold Nano-islands (Au-NIs) structures. Different concentrations of miR-21 (from zepto -molar to micro range) in both standard solution and blood serum samples were measured to test the sensitivity of biosensor. A high surface-area-to-volume ratio of nanostructures embellished on the FTO electrodes increases the chance of immobilization of the thiol modified capture probe (anti-miR-21 or cap-21). The Au-nanostructures surface modification and its ability to hybridize successfully and stably anti-miR-21 and miR-21 confirmed by electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV) electrochemical techniques. The results showed that the linear detection range of the biosensor was from 1.0 zM to 200 nM with a limit of detection (LOD) of 0.12 zM which revealed a very high sensitivity. The selectivity of the biosensor was also investigated and confirmed by detecting miR-9 and miR-486. Corresponding results revealed that the biosensor discriminated target miR-21 from non-complementary miR-21 and showed high selectivity and specificity. Our results also revealed that this platform is a promising substrate to quantitative analysis of miR-21 in physiological samples and could be used for biomedical research and point-of-care (POC) diagnosis. Straightforward and robust Au-NIs surface fabricated without surfactant and stabilizer additive, with plenty of anchors for ssDNA immobilization, as well as well-established hybridization and immobilization procedures, plus high electron transfer rate ability in comparison to bare FTO electrodes are among attractive and suitable novelty of this study.

An amylopullulanase (L14-APU) from an Iranian thermophilic bacterium was purified and the effect of acarbose, as a general inhibitor of α-amylases, on pullulan and starch hydrolysis catalyzed by L14-APU was investigated. The inhibition is a competitive type whereas inhibition constants for pullulan and starch are 99 µM and 72 µM, respectively. Investigation of the reaction rate in a system contains competitive substrates and the inhibition type of acarbose in presence of different substrates suggests that L14-APU possesses only one active site for two activities. The analysis of metal ions and other reagents effects has shown that Ca2+, Mg2+, Mn2+ and Co2+ enhanced both activities of the enzyme while N-bromosuccinimide treatment leads to the complete inactivation of the enzyme. The enzyme activity increased in the presence of low concentration of SDS as a surfactant.

The protein folding kinetics of hen egg white lysozyme (HEWL) was studied using experimental and bioinformatics tools. The structure of the transition state in the unfolding pathway of lysozyme was determined with stopped-flow kinetics using intact HEWL and its chemically modified derivative, in which six lysine residues have been modified. The overall consistency of φ-value (φ ≈ 1) indicates that lysine side chains interactions are subject to breaking in the structure of the transition state. Following experimental evidences, multiple sequence alignment of lysozyme family in vertebrates and exact structural examination of lysozyme, showed that the α-helix in the structure of lysozyme has critical role in the unfolding kinetics.

Abstract: For the first time, a polygalacturonase from the culture broth of Tetracoccosporium sp. was isolated and incubated at 30°C in an orbital shaker at 160 rpm for 48h. The enzyme was purified by ammonium sulfate precipitation and two-step ion-exchange chromatography and had an apparent molecular mass of 36 kDa, as shown by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Its optimum activity was at pH 4.3 and 40°C, and the K m and V max values of this enzyme (for polygalacturonic acid) were 3.23 mg/mL and 0.15 μmol/min, respectively. Ag+, Co2+, EDTA, Tween-20, Tween-80, and Triton X-100 stimulated polygalacturonase activity whereas Al3+, Ba2+, Ca2+, Fe2+, Fe3+, Ni2+, Mg2+, Mn2+, and SDS inhibited it. In addition, iodoacetamide and iodoacetic acid did not inhibit enzyme activity at a concentration of 1 mM, indicating that cysteine residues are not part of the catalytic site of polygalacturonase. We studied the kinetic properties and thermal inactivation of polygalacturonase. This enzyme exhibited a t 1/2 of 63 min at 60°C and its specific activity, turnover number, and catalytic efficiency were 6.17 U/mg, 113.64 min−1, and 35.18 mL/(min·mg), respectively. The activation energy (ΔE #) for heat inactivation was 5.341 kJ/mol, and the thermodynamic activation parameters ΔG #, ΔH #, and ΔS # were also calculated, revealing a potential application for the industry.

Two Bacillussp. strains, HR-08 and KR-8102, isolated from soil of the west and north parts of Iran were screened on gelatin agar medium for their ability to produce alkaline protease. The enzymes were active in a wide pH range (6.0–11.0) and stable in the alkaline range (7.0–12.0). The optimum temperatures for the protease from HR-08 and KR-8102 were 65 and 50°C, respectively. The irreversible thermoinactivation of HR-08 and KR-8102 proteases showed that the stability of HR-08 enzyme was higher than that of KR-8102 and the half-lives of these enzymes were 95 and 32 min at 50°C, respectively. In the presence of 10 mMCa2+, HR-08 retained 100, 90, and 20% of its initial activity after heating for 30 min at 50, 60, and 70°C, respectively. Enzymes were inhibited by phenylmethylsulfonyl fluoride and iodoacetate. After inhibition by iodoacetate, both enzymes were reactivated by dithiothreitol. These data show that the enzymes seem to be thiol-dependent serine alkaline proteases. The enzymes especially from HR-08 were stable in the presence of H2O2, surfactants, and local detergents; their activities were enhanced in the presence of 5 mMFe2+; and the presence of 5mMmetal ions such as Mg2+, Cu2+, and Mn2+produced almost no effect.

The selective toxicity of depressant scorpion neurotoxins to insects is useful in studying the insect sodium channel gating, as well as being relevant to several other applications. In order to carry out structure/activity studies, the functional expression of such polypeptides is required. In the work reported here, the cDNA of a new peptide from the venom of the scorpion Buthotus saulcyi was cloned and sequenced. It codes for a 64 residues peptide (BsaulI) with 8 highly-conserved cysteines. This peptide shares high sequence similarity with depressant insect toxins of other scorpion species. Large amounts of insoluble BsaulI protein were expressed in Escherichia coli. Purification of this peptide was carried out under denaturing conditions. Renaturation was performed by pulsed dilution of the denatured BsaulI in the refolding buffer. Production of refolded Bsaul1, however, is approximately an order of magnitude higher than that obtained with similar scorpion depressant toxins. Intrinsic fluorescence, far-UV circular dichroism spectra and biological activity assays indicate that the peptide adopts a folded structure.

We hereby report on a mutational analysis of a novel natriuretic peptide (PNP), recently isolated by us from the Iranian snake venom. The PNP variant (mutPNP) with four substitutions (G16T, K18S, R21S, G23R) and a disulfide bonded ring shortened by 3 residues. mutPNP peptide was expressed in pET32 and purified by affinity separation on nickel resin followed by RP-HPLC chromatography. The conformation of mutPNP was characterized in solution by 1H nuclear magnetic resonance spectroscopy, where it was found that the 14-residue disulfide bonded ring, like the 17- residue ring in PNP, retains a high degree of conformational flexibility. The conformation of mutPNP bound to NPR-C receptor was predicted by homology protein structure modeling. When injected intravenously into rats, mutPNP, in contrast to PNP had no physiological effect on blood pressure or on diuresis. The loss of physiological activity is explained in terms of the modeled bound conformation and the ensemble of solution conformations obtained using the NMR constraints.

Alkaline solutions containing both silicate and aluminate ions are of considerable research interest inter aliabecause of their involvement in the synthesis of zeolites. 27Al NMR spectra of alkaline aluminosilicate solutions generally show a maximum of five broad bands. In the present work, we use 27Al NMR to characterize aluminosilicate solutions with different Al/Si ratios using 2-hydroxyethyl(trimethyl)ammonium as a cation template, no alkaline metals are used for preparation of aluminosilicate solutions. To understand the reaction between silicate and aluminate ions in this system, the evolutions of 27Al NMR spectra with time are investigated.

A new α-amylase was extracted from a recently found strain of Bacillussp. and purified by ion-exchange chromatography. Sodium dodecyl sulfate polyacrylamide gel electrophoresis showed a single band for the purified enzyme with an apparent molecular weight of 59 kDa. The optimum temperature and pH range of the enzyme were 40–60°C and 4.5–7.5, respectively, and its activation energy was 1.974 kcal/mol. The Kmvalue for the enzyme activity on solubie starch was 4 mg/mL, and the Tmvalues obtained from the circular dichroism (CD) results of thermal unfolding were 78.7 and 80.2°C in the absence and presence of the calcium, respectively. The enzyme was almost completely inhibited by the addition of Fe3+, Mn2+, and Zn2+and was activated by EDTA, Cr3+, and Al3+. Moreover, it was partially inhibited by Ca2+, Ba2+, Ni2+, and Co2+. Proteolytic digestion of the enzyme using trypsin combined with results from Tmusing CD and irreversible thermoinactivation suggests that this enzyme can be considered a moderate thermophile with both mild flexibility and rigidity.

The first highly resolved ²⁷Al NMR spectra of alkaline aluminosilicate solutions have been recorded and are discussed. The linewidths and number of resolved lines are shown to depend critically on several factors, especially the pH and Si∶Al ratio. At least thirteen separate peaks or bands are observed at pH ≈ 10.35 and Si∶Al = 1∶1. A substantial range of anionic species, comparable to those found for alkaline silicate solutions, is thus shown to exist in dynamic equilibrium. Tentative assignments of some bands are presented, based on ²⁷Al and ²⁹Si shift comparability, ²⁷Al linewidths and ²⁷Al spin–lattice relaxation measurements. Relative intensities of the various ²⁷Al signals are given for the pH ≈ 10.35 solution.

A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair‐information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60%, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case. Proteins 2001;42:452–459. © 2001 Wiley‐Liss, Inc.

A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair‐information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60%, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case. Proteins 2001;42:452–459. © 2001 Wiley‐Liss, Inc.

Drug delivery vehicles based on magnetic nanoparticles present a promising strategy for cancer treatment, due to controlled targeted treatment, high loading efficiency, and biosafety as compared to traditional drug delivery approaches. In the present study, superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs) were synthesised by a co-precipitation approach, stabilised with dextran (DEX), and successfully conjugated with folate (FA) for delivery of camptothecin (CPT) in prostate cancer cells. Size and other characteristics of the modified nanoparticles were measured using scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic light scattering (DLS), and zeta-potential. The results demonstrated that the prepared FA-DEX-SPIONs were spherical in shape with an average diameter of 63.31 nm. They had anticancer activity with high CPT loading efficiency in AT3B-1cancer cells, enabling the therapeutic activity of the drug via its active delivery and release at 37 °C in phosphate and citrate buffer solutions. MTT results exhibited no cytotoxicity on rat androgen independent prostate cancer (AT3B-1) and normal human prostate (RWPE-1) cells. In conclusion, FA-DEX-SPION composite is a promising candidate that could be used for the targeted release of CPT anti-cancer drug.