{alpha}-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A

Conformation of the C-peptide fragment of RNase A is calculatedby Monte Carlo simulated annealing. We adopt the total potentialenergy as given by the sum of generic interatomic energies whoseparameters are determined separately for each amino acid withoutreferring to the empirical structure of the C-peptide. The simulationis carried out in a completely unrestricted way without imposingany weight towards given final destinations. Starting from completelyrandom initial conformations and minimizing the total potentialenergy with respect to main-chain dihedral angles and side-chaintorsion angles, we have obtained partial -helix structure witha high probability ({small tilde}40%). The energetically mostfavourable structure exhibits a 2.5-turn -helix at the locationidentical with that of the 3-turn -helix in the native enzymemolecule. Classification of conformations obtained in the simulationinto clusters of similar structure shows that our simulationindeed predicts the -helix structure for the isolated C-peptidewith specific charged residues. The results of simulation withvarious amino acid substitutions are also found to be consistentwith the experimental implication for the importance of intramolecularionic interactions for -helix stability for this peptide.     

Effects of caloric restriction on development of the proximal growth plate and metaphysis of the caput femoris in spontaneously hypertensive rats: microscopic and computer-assisted image analyses

We previously demonstrated that caloric restriction (CR) reduced the prevalence of osteonecrosis in caput femoris of spontaneously hypertensive rats (SHR), a model of human Perthes' disease. The effects of CR on the development and pathology in the proximal femoral growth plate (GP) and adjacent structures in SHR were investigated by morphometric and computer-assisted image analyses. From 6 weeks of age, the food intake of SHR was restricted to 65% of the mean intake of ad libitum fed control SHR (SHR-AL). Wistar Kyoto rats (WKY), from which the SHR strain was isolated, fed ad libitum were also included as controls. CR reduced prevalence of chondromucinous degeneration and dysarray of cartilage cell columns in the GP, becoming prevalent between 10 and 20 weeks in the SHR-AL group, attaining the same levels of the WKY group. Thicknesses of non-calcifying cell columns in the GP were greater in the SHR-AL than WKY group; CR slightly reduced the thickness, but incompletely. Thicknesses of calcifying cell columns did not significantly differ among the three groups. CR decreased volume density and mean thicknesses of the trabecular bone in areas adjacent to GPs, and was greater in the SHR-AL than the WKY group. The present morphologic analysis suggested that CR ameliorates dysplastic changes of trabecular bones in areas adjacent to the GP, rather than modulating the ossification process in the GP. The CR paradigm might give insight into the pathogenesis of, and a therapeutic strategy for, human Perthes' disease.     

Potent antibacterial peptides generated by pepsin digestion of bovine lactoferrin.

The antibacterial properties of enzymatic hydrolysates of bovine lactoferrin were examined to determine whether active peptides are produced from this protein. Hydrolysates prepared by cleavage of lactoferrin with porcine pepsin, cod pepsin, or acid protease from Penicillium duponti showed strong activity against Escherichia coli O111, whereas hydrolysates produced by trypsin, papain, or other neutral proteases were much less active. Low molecular weight peptides generated by porcine pepsin cleavage of lactoferrin showed broad-spectrum antibacterial activity, inhibiting the growth of a number of Gram-negative and Gram-positive species, including strains that were resistant to native lactoferrin. The antibacterial potency of the hydrolysate was at least eightfold greater than that of undigested lactoferrin with all strains tested. The active peptides retained their activity in the presence of added iron, unlike native lactoferrin. The effect of the hydrolysate was bactericidal as indicated by a rapid loss of viability of E. coli O111. The lactoferrin hydrolysate described in the present study has commercial value as a natural preservative agent for use in foods and cosmetics, and as a functional component of new clinical foods for prevention or treatment of gastrointestinal disease.     

Sequential molecularly targeted drug therapy including axitinib for a patient with end‐stage renal failure and metastatic renal cell carcinoma

A 62‐year‐old male patient with end‐stage renal disease and metastatic renal cell carcinoma (RCC) was referred to our hospital. Sequential targeted therapy consisting of sorafenib, sunitinib, and everolimus was administered, but the patient's disease gradually progressed. Axitinib was subsequently administered at a decreased dose of 6 mg/day for 2 weeks, after which the dose was escalated to 10 mg/day. Axitinib therapy was maintained for a total of 6 months without severe adverse effects. Sequential molecularly targeted drug therapy including axitinib, with careful monitoring, is one possible treatment option for patients with metastatic RCC with renal impairment.     

Immobilization of cholesterol esterase in mesoporous silica materials and its hydrolytic activity toward diethyl phthalate

Cholesterol esterase (CE, cholesteryl ester hydrolase, EC 3.1.1.13) from porcine pancreas (molecular weight 400–500 kDa) exhibits hydrolytic activity toward various toxic organic phthalate esters. CE was confined in the nanospace (diameter 3–30 nm) of five types of mesoporous silica (MPS) that differ in structural properties such as pore diameter, pore volume, and particle morphology. These structural properties were characterized by transmission electron microscopy, small-angle X-ray diffraction, N₂ adsorption–desorption experiments, solid-state ¹³C nuclear magnetic resonance (NMR), and solid-state ²⁹Si NMR. Catalytic activities of immobilized and free CE were evaluated by the hydrolysis of diethyl phthalate in phosphate buffer solutions containing an organic cosolvent. Optimal activity recovery was achieved when CE was immobilized in n-decane-functionalized MPS, which had a large pore size (22.5 nm). The immobilization also protected against effects of temperature within the range 30 °C–60 °C; CE immobilized in n-decyl-functionalized MPS exhibited better thermal stability than in non-functionalized MPS or free CE. Moreover, it retained approximately 60% of its catalytic activity even after six catalytic cycles.     

On non‐linear transformations for accurate numerical evaluation of weakly singular boundary integrals

This paper presents a study of the performance of the non‐linear co‐ordinate transformations in the numerical integration of weakly singular boundary integrals. A comparison of the smoothing property, numerical convergence and accuracy of the available non‐linear polynomial transformations is presented for two‐dimensional problems. Effectiveness of generalized transformations valid for any type and location of singularity has been investigated. It is found that weakly singular integrals are more efficiently handled with transformations valid for end‐point singularities by partitioning the element at the singular point. Further, transformations which are excellent for CPV integrals are not as accurate for weakly singular integrals. Connection between the maximum permissible order of polynomial transformations and precision of computations has also been investigated; cubic transformation is seen to be the optimum choice for single precision, and quartic or quintic one, for double precision computations. A new approach which combines the method of singularity subtraction with non‐linear transformation has been proposed. This composite approach is found to be more accurate, efficient and robust than the singularity subtraction method and the non‐linear transformation methods. Copyright © 2001 John Wiley & Sons, Ltd.     

Enhanced multiobjective particle swarm optimization in combination with adaptive weighted gradient-based searching

This article proposes a new multiobjective optimization method for structural problems based on multiobjective particle swarm optimization (MOPSO). A gradient-based optimization method is combined with MOPSO to alleviate constraint-handling difficulties. In this method, a group of particles is divided into two groups—a dominated solution group and a non-dominated solution group. The gradient-based method, utilizing a weighting coefficient method, is applied to the latter to conduct local searching that yields superior non-dominated solutions. In order to enhance the efficiency of exploration in a multiple objective function space, the weighting coefficients are adaptively assigned considering the distribution of non-dominated solutions. A linear optimization problem is solved to determine the optimal weighting coefficients for each non-dominated solution at each iteration. Finally, numerical and structural optimization problems are solved by the proposed method to verify the optimization efficiency.     

Enhanced thermal stability of laccase immobilized on monolayer-modified nanoporous Au

Nanoporous Au was fabricated by the dealloying of Au-Ag alloy in nitric acid, and was modified with a self-assembled monolayer (SAM) of 4-aminothiophenol, for the enhancement of high-temperature activity of immobilized laccase. Immobilized laccase exhibited much higher activity than that of free laccase at > 45 °C. SAM surface modification greatly improved the thermal stability and reusability of immobilized laccase. For example, little degradation in laccase activity when immobilized on SAM-modified nanoporous Au was observed after 2 h incubation at 50 °C. This suggested the nanoporous structure and SAM synergistically prevented the conformational change of laccase, and resulted in the enhancement of high-temperature activity.     

Stress characterization of Si by near-field Raman microscope using resonant scattering

We have developed a tapping-mode scanning near-field optical Raman microscope (SNORM) with a caved and pyramidical probe, using resonant Raman scattering, and have measured the stress distribution of Si. The peak frequency shifts to a lower frequency by 0-0.5 cm(-1) in the area covered by silicon dioxide, whereas it shifts to a higher frequency by 0-0.3 cm(-1) in the area uncovered by silicon dioxide, showing that the areas covered and uncovered by silicon dioxide are under tensile and compressive stresses, respectively. It has been found that compressive stresses of about 0.69 GPa/cm2 are concentrated on the corner of the area uncovered by silicon dioxide. The comparison of stress distributions measured with and without the cantilever shows that the SNORM we developed has a spatial resolution of at least less than 250 nm.     

Quantitative measurements of amino acids by terahertz time-domain transmission spectroscopy

The quantitative analysis of amino acids by terahertz (THz) time-domain absorption spectroscopy is demonstrated. The optical densities of the amino acids were found to be linearly proportional to the concentration. The molar absorption coefficients of L-glutamic acid (L-Glu), L-glutamic acid sodium salt (Na-L-Glu), L-glutamic acid hydrochloric salt (HCl-L-Glu), L-cysteine (L-Cys), and L-histidine (L-His) were calculated by averaging the THz spectra of the amino acids at several different concentrations in approximately the 0.2-1.0 mol L(-1) range. The concentrations of L-Glu, L-Cys, and L-His mixed samples were successfully calculated with errors of less than 11% and 20% when their concentrations were higher than 0.45 and 0.22 mol L(-1), respectively, by using the obtained molar absorption coefficient.