Unfolding events of Chymotrypsin Inhibitor 2 (CI2) revealed by Monte Carlo (MC) simulations and their consistency from structure-based analysis of conformations

We investigated the behavior of the conformations of Chymotrypsin Inhibitor (CI2) from the native to the denatured states, obtained in Monte Carlo (MC)/Metropolis simulations, where a low-resolution model is used together with knowledge-based potentials. New conformations starting from the X-ray native structure are generated by random perturbations along with a constraint to increase the radius of gyration. Unfolding is also simulated by unrestrained simulations at a higher temperature. All simulations yield a similar sequence of unfolding events. The preferred pathway starts with loss of native contacts between (N-terminal)-β₃ and continues with β₂-β₃. The persistence of the contacts between β₁ and β₂ at intermediate values of the fraction of native contacts (Q); whereas, highly unfolded conformations with only some helical contacts persisting at low values of Q, are observed. Structure-based analysis of the fluctuations of the unfolded conformations by Gaussian Network Model (GNM) reveals that the termini of the chain—C terminus being more mobile—depict relatively higher flexibility with a native-like hinge near β₂ that divides the structure into two domains. The fluctuations of the two domains are negatively correlated, with partly folded α-helix and a small hydrophobic cluster in the middle of the chain displaying positively correlated fluctuations. The most persistent short-range rotational bond correlations are observed between the residues of α-helix, C terminus of the β₁-part of the reactive site loop, and around the C terminus of the β₂. The latter regions also appear as hot spots; i.e. high frequency fluctuating regions, of the structure surviving in unfolded conformations. The results imply that the unfolded CI2 has an intrinsic ability to undergo correlated fluctuations along with some residual native structure specifically induced by its sequence, consisting at the lowest level of a single hinge.     

Preparation and characterization of Ni-nitrilotriacetic acid bearing poly(methacrylic acid) coated superparamagnetic magnetite nanoparticles

Stable superparamagnetic magnetite (Fe3O4) nanoparticles were synthesized via co-precipitation in the presence of poly(methacrylic acid) (PMAA) in aqueous solution. The polymer coated Fe3O4 nanoparticles were characterized using transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction, thermal analysis, and vibrating sample magnetometry (VSM) techniques. These measurements reveal the presence of magnetite nanoparticles with a size of approximately 8 nm inside the PMAA matrix. The magnetization value of these superparamagnetic nanoparticles at room temperarure and 7 T was measured as about 40 emu/g. PMAA-coated Fe3O4 nanoparticles were further assembled with Ni-chelate through a reaction between a primary amine-bearing NTA (nitrilotriacetic acid) ligand and carboxy-functional groups of PMAA. NTA-PMAA-coated magnetite nanoparticles were then loaded with nickel ions and characterized using FTIR. The average amount of binded Ni on the surface of the NTA-modified PMAA coated Fe3O4 was calculated as 1.65 +/- 0.3 x 10(-6) mol nickel(II) ions per g of the magnetic particles from the inductively coupled plasma optical emission spectroscopy (ICP-OES) measurements.     

Microtubule-based gold nanowires and nanowire arrays

Biological structures are attractive as templates to form nanoscale architectures for electronics because of their dimensions and the ability to interact with inorganic materials. In this study, we report the fabrication and electrical properties of microtubule (MT)-templated Au nanowires, and methods for assembling Au nanowire arrays based on these templates. The adsorption of MTs on silicon substrates is an effective means for preserving the conformation of the MT and provides a convenient platform for electrical measurements. To improve the metallization of MTs, a photochemical route for gold reduction is adapted, which leads to continuous coverage. The conductivity values measured on micrometer-long nanowires are similar to those reported for other biotemplated gold nanowires. A protocol for fabricating arrays of MT-templated gold nanowires is demonstrated.     

Label-free electrochemical hybridization genosensor for the detection of hepatitis B virus genotype on the development of Lamivudine resistance

The resistance analysis related to the hepatitis B virus (HBV) genotyping and treatment procured key information for the study of infected patients. The aim of this study was to develop a novel assay for the voltammetric detection of DNA sequences related to the HBV genotype on the development of lamuvidine resistance by monitoring the oxidation signal of guanine. This new technique not only provides a rapid, cost-effective, simple analysis but also gives information concerning both genotyping and lamivudine resistance. Synthetic single-stranded oligonucleotides ("probe") including YMDD (HBV wild type) YVDD, or YIDD (mutations in the YMDD) variants have been immobilized onto pencil graphite electrodes with the adsorption at a controlled potential. The probes were hybridized with different concentrations of their complementary ("target") sequences such as synthetic complementary sequences, clonned PCR products, or real PCR samples. The formed synthetic hybrids on the electrode surface were evaluated by a differential pulse voltammetry technique using a label-free detection method. The oxidation signal of guanine was observed as a result of the specific hybridization between the probes and their synthetic targets and specific PCR products. The response of the hybridization of the probes with their single-base mismatch oligonucleotides at PGE was also detected. Control experiments using the noncomplementary oligonucleotides were performed to determine whether the DNA genosensor responds selectively. Numerous factors, affecting the probe immobilization, target hybridization, and nonspecific binding events, were optimized to maximize the sensitivity and reduce the assay time. Under the optimum conditions, 457 fmol/mL was found as the detection limit for target DNA. With the help of the appearance of the guanine signal, the new protocol is based on the electrochemical detection of HBV genotype for the development of lamuvidine resistance for the first time. Features of this protocol are discussed and optimized.     

Spectroscopic characterization of Cl-modified Mo/Si:Ti catalysts for oxidative dehydrogenation of propane

In this study, a series of chlorine-modified molybdenum catalysts supported on silica and titania (Si:Ti) mixed oxides were prepared by a modified sol–gel technique. The catalytic performance of the catalysts was tested for the oxidative dehydrogenation (ODH) of propane. Catalysts were characterized by in situ or controlled-atmosphere measurements with XPS, LRS, ESR, and DRIFTS techniques to elucidate the adsorption and transformation of propane/propylene and the reduction of surface molybdena species over the Si:Ti support. In addition, isotopic labeling studies have been performed to investigate the oxygen mobility and oxygen exchange characteristics and reaction pathways involving propane ODH. These characterization results are correlated with the catalytic reaction performance to achieve a better understanding of the catalytic behavior of chlorine-modified Mo/Si:Ti catalysts.     

Pyrrole/N‐p‐toluenepyrrole copolymers in the presence of surfactants: A promising material for glucose sensing

In this study, pyrrole/N‐para‐toluenpyrrole (Py/NptPy) copolymers were synthesized by chemical oxidative polymerization method. The effects of different kinds of (anionic, cationic, and nonionic) surfactants on the properties of copolymer were investigated. The structural, morphological, thermal, and conductivity properties of the copolymers were investigated by using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and the four‐probe measurement device respectively. FTIR spectra of copolymers synthesized in different environments that support the formation of copolymer. SEM results show that the morphologies of copolymers synthesized in the presence of surfactant are more homogeneous and the particle sizes are smaller than that of polypyrrole (PPy). TGA results revealed that the thermal stabilities of Py/NptPy‐NaDBS (400°C) and Py/NptPy‐Tween 20 (260°C) copolymers were higher than surfactant free Py/NptPy copolymer (180°C) according to their initial decomposition temperatures. It was determined that the conductivity values of copolymers were higher than PNptPy. Glucose sensor properties of copolymer synthesized in the presence of tetradecylthreemethyl ammonium bromide (TTAB) were investigated with cyclic voltammetry (CV) method. Michaelis–Menten constant of Py/NptPy‐TTAB copolymer modified electrochemical biosensor was calculated as 5.30 mM. POLYM. ENG. SCI. 56:995–1003, 2016. © 2016 Society of Plastics Engineers     

One-step synthesis of hybrid magnetic material based on polyphenoxazine and bimetallic Co–Fe nanoparticles

Polymer Bulletin - A simple method for preparation of hybrid magnetic nanocomposites consisting of bimetallic Co–Fe nanoparticles and polyphenoxazine (PPOA) is described. The nanocomposites...     

A new causal discovery heuristic

Probabilistic methods for causal discovery are based on the detection of patterns of correlation between variables. They are based on statistical theory and have revolutionised the study of causality. However, when correlation itself is unreliable, so are probabilistic methods: unusual data can lead to spurious causal links, while nonmonotonic functional relationships between variables can prevent the detection of causal links. We describe a new heuristic method for inferring causality between two continuous variables, based on randomness and unimodality tests and making few assumptions about the data. We evaluate the method against probabilistic and additive noise algorithms on real and artificial datasets, and show that it performs competitively.