On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Electrical Network of Single‐Crystalline Metal Oxide Nanoclusters Wired by π‐Molecules

In a mixed‐valence polyoxometalate, electrons are usually delocalized within the cluster anion because of low level of inter‐cluster interaction. Herein, we report the structure and electrical properties of a single crystal in which mixed‐valence polyoxometalates were electrically wired by cationic π‐molecules of tetrathiafulvalene substituted with pyridinium. Electron‐transport characteristics are suggested to represent electron hopping through strong interactions between cluster and cationic π‐molecules.     

Simultaneous detection of ammonia and humidity using transmission surface plasmon resonance technique

Abstract

Gas sensing by using the transmission surface plasmon resonance (T-SPR) technique was demonstrated. Polyacrylic acid (PAA)/5-nm-thick gold/40-nm-thick silver/polycarbonate grating substrate structure (Sensor A) responded to ammonia; however, it exhibited a strong humidity dependence. Polyvinyl alcohol (PVA)/5-nm-thick gold/40-nm-thick silver/polycarbonate grating substrate structure (Sensor B) as the sensing material was also prepared and it mainly responded to humidity. The T-SPR properties of Sensors A and B were observed simultaneously by a stacking arrangement that enabled us to obtain the responses by using a single spectrophotometer. The ammonia concentration under various humidity conditions could be accurately obtained by simultaneous measurement of Sensors A and B.     

Antibacterial metal implant with a TiO2‐conferred photocatalytic bactericidal effect against Staphylococcus aureus

Photocatalysis with anatase Titanium dioxide (TiO₂) under ultraviolet A (UVA) has a well recognized bactericidal effect. There have been a few reports, however, on the effects of photocatalysis on bio‐implant‐related infections. The purpose of present study was to evaluate the photocatalytic bactericidal effects of anatase TiO₂ on Staphylococcus aureus (S. aureus) associated with surgical site infections. TiO₂ films were synthesized on commercially pure titanium substrates and SUS316 stainless steel using a plasma source ion implantation method followed by annealing. The chemical composition of the surface layers was determined using GXRD and XPS. The disks were seeded with cultured S. aureus and exposed to UVA illumination from black light. The bactericidal effect of the TiO₂ films was evaluated by counting the survived colonies statistically. A structural gradient anatase type TiO₂ layer formed on all substrates. The viability of the bacteria on the photocatalytic TiO₂ film coated on titanium was suppressed to 7.0% at 30 minutes and 5.5% at 45 minutes, whereas that on a similarly coated stainless steel was suppressed to 45.8% at 30 minute and 28.6% at 45 minutes (ANOVA: p < 0.05). Complete bacterial inactivation was achieved after 90 minutes on titanium and after 60 minutes on stainless steel. The photocatalytic bactericidal effect of TiO₂ is useful for sterilizing the contaminated surfaces of bioimplants. Copyright © 2008 John Wiley & Sons, Ltd.     

Inter-atomic distance and temperature dependence of correlation effects among thermal displacements

Diffuse neutron scattering from a powder AgCl was measured from 10 to 260 K. The correlation effects among thermal displacements of atoms were obtained from the diffraction data. The values of the correlation effects decrease rapidly with the increase of the inter-atomic distance. The values also decrease with the decrease of temperature. The similar tendency was also obtained in AgBr and CuI. The temperature dependence of the values of correlation effects agrees with the result by a simple Debye model of lattice vibrations.     

Kinetic studies on saponification of ethyl acetate using an innovative conductivity‐monitoring instrument with a pulsating sensor

An innovative conductometric measurement technique using a nonconventional but high‐performance (high‐precision, high‐resolution, rapid response features for online graphic display) in house–built pulsating conductivity monitoring instrument has been deployed to study the kinetic behavior during the reaction of ethyl acetate and NaOH. A laboratory‐made constant temperature reaction bath with the facility of continuous stirring of solution for homogeneous mixing was used to carry out experiments at desired solution temperatures. Rate constants of the saponification reaction in the temperature range at various temperatures (30–55°C) were determined, and the results were compared with the reported values. Although the reported data exhibit wide scatter, our data are in agreement with some of the literature data. From these data, thermodynamic parameters such as activation energy, activation enthalpy, activation entropy, and activation free energy have been evaluated. With the introduction of this novel conductometric measurement technique, the determination of rate constants at various solution temperatures becomes much simpler and faster. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 648–656, 2011     

A novel injection method for high-speed proteome analysis by capillary electrophoresis

We have developed a new sample injection method for capillary electrophoresis (CE) that reduces the required migration time. We demonstrated a pressurization technique that was performed with buffer in the outlet after the electrokinetic sample injection with no buffer in the outlet. To reduce the migration time, the sample injection had to be performed with no buffer in the outlet; water should be pressurized while the buffer is in the outlet. Though the resolution was slightly decreased using this method, the addition of a separation carrier (curdlan) to the run buffer restored the resolution without delaying the migration time. The use of our new sample injection method combined with our high-quality separation carrier will enable us to improve the efficiency of the high-throughput screening (HTS) system for proteome analysis.