Investigation of protein-protein interactions: multibody docking, association/dissociation kinetics and macromolecular crowding

Protein-protein interactions are central to understanding how cells carry out their wide array of functions and metabolic procedures. Conventional studies on specific protein interactions focus either on details of one-to-one binding interfaces, or on large networks that require a priori knowledge of binding strengths. Moreover, specific protein interactions, occurring within a crowded macromolecular environment, which is precisely the case for interactions in a real cell, are often under-investigated. A macromolecular simulation package, called BioSimz, has been developed to perform Langevin dynamics simulations on multiple protein-protein interactions at atomic resolution, aimed at bridging the gaps between structural, kinetic and crowding studies on protein-protein interactions. Simulations on twenty-seven experimentally determined protein-protein interactions, indicated that the use of contact frequency information of proteins forming specific encounters can guide docking algorithms towards the most likely binding regions. Further evidence from eleven benchmarked protein interactions showed that the association rate constant of a complex, kon, can be estimated, with good agreement to experimental values, based on the retention time of its specific encounter. Performing these simulations with ten types of environmental protein crowders, it suggests, from the change of kon, that macromolecular crowding improves the association kinetics of slower-binding proteins, while it damps the association kinetics of fast, electrostatics-driven protein-protein interactions. It is hypothesised, based on evidence from docking, kinetics and crowding, that the dynamics of specific protein-protein encounters is vitally important in determining their association affinity. There are multiple factors by which encounter dynamics, and subsequently the kon, can be influenced, such as anchor residues, long-range forces, and environmental steering via crowders’ electrostatics and/or volume exclusion. The capacity of emulating these conditions on a common platform not only provides a holistic view of interacting dynamics, but also offers the possibility of evaluating and engineering protein-protein interactions from aspects that have never been opened before

The Chinese Hospitality Industry: A perspective article

This paper illustrates the logics shifting in the Chinese hotel industry since1949 and offers a better understanding of how and why the Chinese hotel industry has evolved into its present situation. The logic evolution and future trends in this market were also discussed

Morphology and Orientation Selection of Non-Metallic Inclusions in Electrified Molten Metal

The effect of electric current on morphology and orientation selection of non-metallic inclusions in molten metal has been investigated using theoretical modelling and numerical calculation. Two geometric factors, namely the circularity (fc) and alignment ratio (fe) were introduced to describe the inclusions shape and configuration. Electric current free energy was calculated and the values were used to determine the thermodynamic preference between different microstructures. Electric current promotes the development of inclusion along the current direction by either expatiating directional growth or enhancing directional agglomeration. Reconfiguration of the inclusions to reduce the system electric resistance drives the phenomena. The morphology and orientation selection follows the routine to reduce electric free energy. The numerical results are in agreement with our experimental observations

Domain movement in rabbit muscle adenylate kinase might involve proline isomerization

AbstractThe fluorescence probe, 8-anilino-1-naphthalenesulfonic acid (ANS), was used to monitor the induced-fit conformational movement in rabbit muscle adenylate kinase. In 50 mM Tris-HCl buffer (pH 8.1), the time course of ANS binding to rabbit muscle adenylate kinase is a biphasic process. The fast phase completes within the dead-time of the stopped-flow equipment used (about 15 ms), while the slow phase ends in about 10 minutes. In the presence of 2.0 μM peptidyl prolyl cis/trans-isomerase, the rate constant of the slow phase reaction is accelerated about 2.4-fold, suggesting that the domain movement during ANS binding to rabbit muscle adenylate kinase may involve proline isomerization. The activation energy of the slow phase was determined to be 74.6 kJ/mol, which is comparable to the activation energy of proline cis/trans-isomerization (about 80 kJ/mol)

A failure study of the railway rail serviced for heavy cargo trains

AbstractIn this case study, a failed railway rail which was used for heavy cargo trains was investigated in order to find out its root cause. The macroscopic beach marks and microscopic fatigue striations were not observed by macro and microscopic observations. The chevron patterns were observed by macro observations. The crack origin was at the tip of chevron patterns. The fan-shaped patterns, cleavage step and the river patterns were observed at the crack origin, which demonstrated the feature of cleavage fracture. The metallurgical structures at the crack origin were pearlite and ferrite networks. The crack is supposed to be initiated from the weaker ferrite networks. Given all of that, the failed railway rail is considered to be caused by overload. It is of great importance to improve the welding technology, and control the load of train in order to prevent similar failure in future

Effects of yeast culture on broiler growth performance, nutrient digestibility and caecal microbiota

This study was conducted to evaluate the effects of yeast culture (YC) supplementation on the growth performance, apparent nutrient digestibility and caecal microflora of broiler chickens. A total of 360 one-day-old Arbor Acres broiler chickens were randomly assigned to six dietary treatments containing 0.2%, 0.4%, 0.6%, 0.8% and 1% YC. The experiment lasted for 42 days. Diet and faecal samples were collected for analysis of dry matter, crude protein, ether extract, calcium and phosphorus. Caecal microbiota on days 21 and 42 were measured using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR. Dietary supplementation with YC did not affect feed intake. On day 42, the 0.8% YC group showed optimal growth and feed efficiency, as well as higher levels of apparent digestibility of ether extract, calcium and phosphorus. On day 21, both 0.8% and 1% YC groups exhibited a significant increase in Ruminococcus, Propionibacterium clostridiales, and Bifidobacterium density. The density of Bacteroides in the YC groups was significantly higher than that of the control group. On day 42, the densities of Bacteroides, Sphingomonas and Bifidobacterium were higher in the 0.8% YC group, whereas a significant decrease was observed in the number of Enterobacteriaceae. These results serve as evidence that dietary supplementation with 0.8% YC not only moderately optimized the feed efficiency and the apparent digestibility of ether extract, calcium and phosphorus, but also positively influenced the caecal bacterial density and diversity in broiler chickens.Keywords: Arbor Acres broiler, caecal microflora, yeast culture supplementatio

Characterization study of GaN-based epitaxial layer and light-emitting diode on nature-patterned sapphire substrate

[[abstract]]Chemical wet etching on c-plane sapphire wafers by three etching solutions (H3PO4, H2SO4, and H3PO4/H2SO4 mixing solution) was studied. Among these etching agents, the mixing H3PO4/H2SO4 solution has the fastest etching rate (1.5 μm/min). Interestingly, we found that H2SO4 does not etch the c-plane sapphire wafer in thickness; instead, a facet pyramidal pattern is formed on the c-plane sapphire wafer. GaN light-emitting diode (LED) epitaxial structure was grown on the sapphire wafer with the pyramidal pattern and the standard flat sapphire wafer. X-ray diffraction and photoluminescence measurement show that the pyramidal pattern on the sapphire wafer improved crystalline quality but augmented the compressive stress level in the GaN LED epilayer. The horizontal LED chips fabricated on the pyramidal-patterned sapphire wafer have a larger light output than the horizontal LED chips fabricated on the standard flat sapphire wafer by 20%.[[notice]]補正完畢[[incitationindex]]SCI[[booktype]]紙本[[booktype]]電子

Magnetic phase diagram in Eu1−x_{1-x}Lax_xFe2_2As2_2 single crystals

We have systematically measured resistivity, susceptibility and specific heat under different magnetic fields (H) in Eu$_{1-x}$La$_x$Fe$_2$As$_2$ single crystals. It is found that a metamagnetic transition from A-type antiferromagnetism to ferromagnetism occurs at a critical field for magnetic sublattice of $Eu^{2+}$. The jump of specific heat is suppressed and shifts to low temperature with increasing H up to the critical value, then shifts to high temperature with further increasing H. Such behavior supports the metamagnetic transition. Detailed H-T phase diagrams for x=0 and 0.15 crystals are given, and possible magnetic structure is proposed. Magnetoresistance measurements indicate that there exists a strong coupling between local moment of $Eu^{2+}$ and charge in Fe-As layer. These results are very significant to understand the underlying physics of FeAs superconductors.Comment: 5 pages, 4 figure